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Papers by John Tully

Physical Review, 1969

With the ultimate goal of elucidating inelastic processes in molecules, we have developed a pseud... more With the ultimate goal of elucidating inelastic processes in molecules, we have developed a pseudopotential method by which one can compute the wave functions for electron scattering states around atoms, molecules, and their respective ions. The method depends upon ...

The Psychiatrist, 2012

ABSTRACT Aims and Method High rates of metabolic syndrome exist among patients on clozapine. Moni... more ABSTRACT Aims and Method High rates of metabolic syndrome exist among patients on clozapine. Monitoring its parameters facilitates interventions which may alleviate negative health consequences. We completed an audit of the monitoring of the parameters of metabolic syndrome in patients on clozapine. The results were compared with the Maudsley Guidelines for monitoring in patients on any antipsychotic medication. Results Initial audit showed high overall rates of concordance with guidelines for the frequency of measurement of blood pressure (91.8%), but much lower rates for measuring fasting blood glucose (43.2%) and lipid profile (52.7%), and no record of analysis of waist circumference. This prompted development of a formal protocol for measuring parameters. Repeat audit after 1 year showed marked improvement in rates of measurement. Clinical implications Implementation of relatively straightforward measures, such as the introduction of a one-page form on which to record parameters, can lead to a much improved rate of monitoring for metabolic syndrome. This should in turn prompt therapeutic interventions, which are discussed.

The Journal of Physical Chemistry C, 2015

CNS Spectrums, 2015

Novel technological interventions are increasingly used in mental health settings. In this articl... more Novel technological interventions are increasingly used in mental health settings. In this article, we describe 3 novel technological strategies in use for management of risk and violence in 2 forensic psychiatry settings in the United Kingdom: electronic monitoring by GPS-based tracking devices of patients on leave from a medium secure service in London, and closed circuit television (CCTV) monitoring and motion sensor technology at Broadmoor high secure hospital. A common theme is the use of these technologies to improve the completeness and accuracy of data used by clinicians to make clinical decisions. Another common thread is that each of these strategies supports and improves current clinical approaches rather than drastically changing them. The technologies offer a broad range of benefits. These include less restrictive options for patients, improved accountability of both staff and patients, less invasive testing, improved automated record-keeping, and better assurance reporting. Services utilizing technologies need also be aware of limitations. Technologies may be seen as unduly restrictive by patients and advocates, and technical issues may reduce effectiveness. It is vital that the types of technological innovations described in this article should be subject to thorough evaluation that addresses cost effectiveness, qualitative analysis of patients' attitudes, safety, and ethical considerations.

The British journal of psychiatry : the journal of mental science, 2014

Electronic monitoring has been used in criminal justice and some health settings for three decade... more Electronic monitoring has been used in criminal justice and some health settings for three decades. Technological interventions are becoming more common in psychiatry, but may be a cause for ethical concerns and controversy. We discuss electronic monitoring as an aid to security and public safety in a forensic setting.

Proceedings of the National Academy of Sciences of the United States of America, Jan 22, 2014

We present measurements of rate constants for thermal-induced reactions of the 11-cis retinyl chr... more We present measurements of rate constants for thermal-induced reactions of the 11-cis retinyl chromophore in vertebrate visual pigment rhodopsin, a process that produces noise and limits the sensitivity of vision in dim light. At temperatures of 52.0-64.6 °C, the rate constants fit well to an Arrhenius straight line with, however, an unexpectedly large activation energy of 114 ± 8 kcal/mol, which is much larger than the 60-kcal/mol photoactivation energy at 500 nm. Moreover, we obtain an unprecedentedly large prefactor of 10(72±5) s(-1), which is roughly 60 orders of magnitude larger than typical frequencies of molecular motions! At lower temperatures, the measured Arrhenius parameters become more normal: Ea = 22 ± 2 kcal/mol and Apref = 10(9±1) s(-1) in the range of 37.0-44.5 °C. We present a theoretical framework and supporting calculations that attribute this unusual temperature-dependent kinetics of rhodopsin to a lowering of the reaction barrier at higher temperatures due to en...

Optics Express, 2013

A dynamic etching approach is proposed through the appropriate variation of etchant composition r... more A dynamic etching approach is proposed through the appropriate variation of etchant composition ratio during the etching process, resulting in the parabolic shape of optical fiber nano-probe with a favorable changing of cone angle. The probe formation mechanism is thoroughly analyzed to illustrate the controllability and simplicity of this method. Optical properties of as-made probes are simulated and experimentally characterized and compared with the linear shape probes of different cone angles. It shows that the parabolic shape probes are superior to the linear shape ones with respect to the transmission efficiency and light focusing capability.

Advances in Mental Health and Intellectual Disabilities, 2012

ABSTRACT Purpose ‐ The Diagnostic Criteria for Psychiatric Disorders for Use with Adults with Lea... more ABSTRACT Purpose ‐ The Diagnostic Criteria for Psychiatric Disorders for Use with Adults with Learning Disabilities/Mental Retardation (DC-LD) was introduced in 2003 in an attempt to improve accuracy of diagnosis in the intellectual disability population. The paper aims to apply this system to a sample of a population with intellectual disability to further investigate its usefulness in the clinical setting. Design/methodology/approach ‐ A sample of 50 patients within an intellectual disability service was identified. Each individual was interviewed by a registrar in psychiatry of intellectual disability in the presence of their key worker or a carer that knew the individual well. Chart notes were extensively reviewed for clearly documented history of psychiatric symptoms and behavioural difficulties. The information gathered was applied as per the DC-LD criteria to identify appropriate diagnoses. Previously documented diagnoses were also recorded for comparison purposes. Findings ‐ There was considerable discrepancy between the rates of psychiatric diagnoses after application of DC-LD and rates of previously documented diagnoses within the sample. Use of DC-LD led to the reclassification of many previously documented diagnoses, mainly as behavioural disorders. There were also discrepancies between rates of diagnosis of pervasive developmental disorders and Alzheimer's disease before and after use of DC-LD. Originality/value ‐ This study adds to the evidence regarding the usefulness of DC-LD in the intellectual disability population and also highlights the shortcomings of non-systematic methods of diagnosis. It was agreed that DC-LD criteria be applied to all service users in this population in the future.

The Journal of Chemical Physics, 2011

A simple and efficient scheme is presented for using different time slices for different degrees ... more A simple and efficient scheme is presented for using different time slices for different degrees of freedom in path integral calculations. This method bridges the gap between full quantization and the standard mixed quantum-classical (MQC) scheme and, therefore, still provides quantum mechanical effects in the less-quantized variables. Underlying the algorithm is the notion that time slices (beads) may be "collapsed" in a manner that preserves quantization in the less quantum mechanical degrees of freedom. The method is shown to be analogous to multiple-time step integration techniques in classical molecular dynamics. The algorithm and its associated error are demonstrated on model systems containing coupled high- and low-frequency modes; results indicate that convergence of quantum mechanical observables can be achieved with disparate bead numbers in the different modes. Cost estimates indicate that this procedure, much like the MQC method, is most efficient for only a relatively few quantum mechanical degrees of freedom, such as proton transfer. In this regime, however, the cost of a fully quantum mechanical simulation is determined by the quantization of the least quantum mechanical degrees of freedom.

The Journal of Chemical Physics, 2009

We have constructed a model Hamiltonian to describe the interaction of a nitric oxide (NO) molecu... more We have constructed a model Hamiltonian to describe the interaction of a nitric oxide (NO) molecule with a Au(111) surface. The diagonal elements of the 2x2 Hamiltonian matrix represent the diabatic potential energy surfaces corresponding to the neutral and negative-ion states of the molecule. A position-dependent off-diagonal element controls the extent of mixing of the two diabatic states. The parameters of the Hamiltonian matrix were determined from ground-state density functional theory calculations, both in the absence and presence of a small applied electric field to perturb the extent of charge transfer to the molecule. The resulting model Hamiltonian satisfactorily reproduces the ab initio results, and scattering simulations of the incident translational energy dependence of trapping probability and final rotational energy of NO agree quite well with experiment. The explicit incorporation of neutral and ionic configurations should serve as a realistic and practical platform for elucidating the importance of charge transfer and nonadiabatic effects at metal surfaces, as well as provide a useful testing ground for the development of theories of nonadiabatic dynamics.

The Journal of Chemical Physics, 2011

A "tiered" appr... more A "tiered" approach to Monte Carlo sampling of nuclear configurations is presented for ab initio, self-consistent field (SCF)-based potentials, including Hartree-Fock and density functional theory. Rather than Metropolis testing only the final SCF energy, individual cycle energies are tested in a tiered fashion, without approximation. Accordingly, rejected configurations are terminated early in the SCF procedure. The method is shown to properly obey detailed balance, and effective modifications are presented for cases in which the initial SCF guess is particularly poor. Demonstrations on simple systems are provided, including an assessment of the thermal properties of the neutral water dimer with B3LYP/6-31++G**. Cost analysis indicates a factor-of-two reduction in SCF cycles, which makes the method competitive with accelerated molecular dynamics sampling techniques, without the need for forces.

Infection Control and Hospital Epidemiology, 2003

Review of health plan administrative data has been shown to be more sensitive than other methods ... more Review of health plan administrative data has been shown to be more sensitive than other methods for identifying postdischarge surgical-site infections (SSIs), but there has not been a direct comparison between this method and hospital-based surveillance for all infections, including those diagnosed before discharge. We compared these two methods for identifying SSIs following coronary artery bypass graft (CABG) procedures. We studied 1,352 CABG procedures performed among members of one health plan from March 1993 through June 1997. Health plan administrative records were reviewed based on claims containing diagnoses or procedures suggestive of infection or outpatient dispensing of antibiotics appropriate for SSI. Hospital-based surveillance information was also reviewed. SSI rates were calculated based on the total events identified by either mechanism. Postdischarge information was reviewed for 328 (85%) of 388 procedures. SSIs were confirmed in 167 patients (13% overall risk of confirmed SSI; range, 3% to 14% in the 5 hospitals). The overall sensitivity of hospital-based surveillance was 49.7% (83 of 167), and that of health plan data was 71.8% (120 of 167). There was no significant difference among hospitals in the sensitivity of either surveillance mechanism. Surveillance based on health plan data identified more postoperative infections, including those occurring before discharge, than did hospital-based surveillance. Screening administrative data and pharmacy activity may be an important adjunct to SSI surveillance, allowing efficient comparison of hospital-specific rates. Interpretation of differences among hospitals' infection rates requires case mix adjustment and understanding of variations in hospitals' discharge diagnosis coding practices.

Infection Control and Hospital Epidemiology, 2004

Nosocomial transmission of malaria is a rare phenomenon in the United States. To describe the pro... more Nosocomial transmission of malaria is a rare phenomenon in the United States. To describe the probable transmission of Plasmodium falciparum malaria from a patient to a healthcare worker and then from the healthcare worker to another patient. Case series. Two community hospitals in Massachusetts. Routine medical and supportive care. Clinical and laboratory evaluation. A nurse developed falciparum malaria after a needlestick injury from a patient with documented falciparum malaria. Three days prior to her diagnosis, she cared for another patient, who subsequently developed falciparum malaria. That patient's parasite isolate genetically matched the nurse's isolate by two independent DNA fingerprinting techniques. After extensive evaluation, we believe that a nurse who had acquired falciparum malaria via needlestick subsequently transmitted malaria to another patient via a break in standard precautions. The implications of this mechanism of transmission are discussed.

Emerging Infectious Diseases, 2004

We evaluated antimicrobial exposure, discharge diagnoses, or both to identify surgical site infec... more We evaluated antimicrobial exposure, discharge diagnoses, or both to identify surgical site infections (SSI). This retrospective cohort study in 13 hospitals involved weighted, random samples of records from 8,739 coronary artery bypass graft (CABG) procedures, 7,399 cesarean deliveries, and 6,175 breast procedures. We compared routine surveillance to detection through inpatient antimicrobial exposure (>9 days for CABG, >2 days for cesareans, and >6 days for breast procedures), discharge diagnoses, or both. Together, all methods identified SSI after 7.4% of CABG, 5.0% of cesareans, and 2.0% of breast procedures. Antimicrobial exposure had the highest sensitivity, 88%-91%, compared with routine surveillance, 38%-64%. Diagnosis codes improved sensitivity of detection of antimicrobial exposure after cesareans. Record review confirmed SSI after 31% to 38% of procedures that met antimicrobial surveillance criteria. Sufficient antimicrobial exposure days, together with diagnosis codes for cesareans, identified more postoperative SSI than routine surveillance methods. This screening method was efficient, readily standardized, and suitable for most hospitals.

Chemical Physics Letters, 2010

Polynomial extrapolation of response ('z-vector') elements is shown to reduce the cost of correla... more Polynomial extrapolation of response ('z-vector') elements is shown to reduce the cost of correlatedwavefunction, classical ab initio molecular dynamics. Demonstrations with resolution-of-the-identity Møller-Plesset perturbation theory (RI-MP2) show that the number of response equation iterations is reduced by a factor of 2-3, thereby enabling accelerated MP2 dynamics. Coupled with previously demonstrated Fock matrix extrapolation, the combined iterative SCF and z-vector calculations are reduced to a minority share of the total calculation. Though demonstrated for MP2, these methods can also be generalized to higher levels of electron correlation or excited state methods.

Chemical Physics, 2000

A combination of molecular dynamics (MD) and Monte Carlo (MC) simulation methods is proposed that... more A combination of molecular dynamics (MD) and Monte Carlo (MC) simulation methods is proposed that may have advantages in some cases over either MD or MC alone. The method is simple: in each step of the algorithm, some of the particles are moved by MC rules and the rest by MD. We prove that the mixed method converges rigorously to

Biophysical Journal, 2010

Forming upon absorption of a UV photon, excited states of DNA are subject to nonadiabatic evoluti... more Forming upon absorption of a UV photon, excited states of DNA are subject to nonadiabatic evolution, via either internal conversion (IC) back to the ground state or mutagenesis. Nonadiabatic processes following the formation of the first singlet excited states, S1, in 10 different small DNA fragmentss4 single 4′H-nucleosides, 2 Watson-Crick base pairs, and 4 nucleotide quartetsshave been investigated. Simulations were done via the nonadiabatic direct trajectory surface hopping semiclassical dynamics. The electronic wave function was obtained with configuration interaction, based on the semiempirical AM1 and PM3 Hamiltonians with fractional orbital occupation numbers. The evolution of the electronic wave function was governed by the time-dependent Schrödinger equation with a locally diabatic representation, intrinsically stable near surface crossings. The nuclei evolved on adiabatic potential energy surfaces, as prescribed by classical Newtonian dynamics, with sudden hops between potential energy surfaces to account for nonadiabatic transitions. The "fewest switches" surface hopping algorithm coupled the quantum and classical parts of the system. The dynamics simulations revealed several routes of nonadiabatic relaxation in these systems, which were not reported previously, and also recovered known routes of IC.

The American Journal of Medicine, 1981

Complications of intravenous therapy with steel needles and small-bore Teflon catheters were comp... more Complications of intravenous therapy with steel needles and small-bore Teflon catheters were compared in a randomized study of 954 cannula insertions. Cannulas were inserted and cared for by an intravenous team following a standard protocol. There were no cases of cannula-related septicemia and only one case of local infection, a cellulitis in the group in which Teflon catheters were used. There was a low incidence of positive semiquantitative cannula cultures in both treatment groups (steel needles 1.5 percent, Teflon catheters 1.4 percent). The risk of phlebitis was significantly greater with Teflon catheters (18.8 percent with Teflon catheters, 8.8 percent with steel needles, adjusted odds ratio 1.87). Steel needles were significantly associated with infiltration (17.9 percent with Teflon catheters, 40.1 percent with steel needles, adjusted odds ratio 0.39). The over-all rate of complications was significantly greater for the group in which steel needles were used (53.8 versus 64.0 percent, adjusted odds ratio 0.72), principally due to the increased risk of infiltration with steel needles. Analysis of the per day risk of infiltration and phlebitis revealed that these relationships were present for each day the cannulas remained in place. We conclude (1) that steel needles and small-bore Teflon catheters can both be used with low risk of infection and (2) that Teflon catheters more frequently cause phlebitis, whereas steel needles infiltrate more readily.

The American Journal of Medicine, 1979

Three patients with clostridial sepsis during or following hepatic arterial infusions for the reg... more Three patients with clostridial sepsis during or following hepatic arterial infusions for the regional chemotherapy of hepatic metastatic tumors are described. In all patients abdominal roentgenograms revealed lucencies in the right upper quadrant consistent with gas-containing hepatic abscesses at the time of clinically apparent sepsis and positive blood cultures. The occurrence of three such cases in one year and the low incidence of clostridial infections in non-catheterized oncology patients at our institution suggest that clostridial infection is a previously unrecognized complication of hepatic arterial infusion chemotherapy. The possible sources of the infecting organisms and pathogenesis of this infection are discussed.

Physical Review, 1969

With the ultimate goal of elucidating inelastic processes in molecules, we have developed a pseud... more With the ultimate goal of elucidating inelastic processes in molecules, we have developed a pseudopotential method by which one can compute the wave functions for electron scattering states around atoms, molecules, and their respective ions. The method depends upon ...

The Psychiatrist, 2012

ABSTRACT Aims and Method High rates of metabolic syndrome exist among patients on clozapine. Moni... more ABSTRACT Aims and Method High rates of metabolic syndrome exist among patients on clozapine. Monitoring its parameters facilitates interventions which may alleviate negative health consequences. We completed an audit of the monitoring of the parameters of metabolic syndrome in patients on clozapine. The results were compared with the Maudsley Guidelines for monitoring in patients on any antipsychotic medication. Results Initial audit showed high overall rates of concordance with guidelines for the frequency of measurement of blood pressure (91.8%), but much lower rates for measuring fasting blood glucose (43.2%) and lipid profile (52.7%), and no record of analysis of waist circumference. This prompted development of a formal protocol for measuring parameters. Repeat audit after 1 year showed marked improvement in rates of measurement. Clinical implications Implementation of relatively straightforward measures, such as the introduction of a one-page form on which to record parameters, can lead to a much improved rate of monitoring for metabolic syndrome. This should in turn prompt therapeutic interventions, which are discussed.

The Journal of Physical Chemistry C, 2015

CNS Spectrums, 2015

Novel technological interventions are increasingly used in mental health settings. In this articl... more Novel technological interventions are increasingly used in mental health settings. In this article, we describe 3 novel technological strategies in use for management of risk and violence in 2 forensic psychiatry settings in the United Kingdom: electronic monitoring by GPS-based tracking devices of patients on leave from a medium secure service in London, and closed circuit television (CCTV) monitoring and motion sensor technology at Broadmoor high secure hospital. A common theme is the use of these technologies to improve the completeness and accuracy of data used by clinicians to make clinical decisions. Another common thread is that each of these strategies supports and improves current clinical approaches rather than drastically changing them. The technologies offer a broad range of benefits. These include less restrictive options for patients, improved accountability of both staff and patients, less invasive testing, improved automated record-keeping, and better assurance reporting. Services utilizing technologies need also be aware of limitations. Technologies may be seen as unduly restrictive by patients and advocates, and technical issues may reduce effectiveness. It is vital that the types of technological innovations described in this article should be subject to thorough evaluation that addresses cost effectiveness, qualitative analysis of patients' attitudes, safety, and ethical considerations.

The British journal of psychiatry : the journal of mental science, 2014

Electronic monitoring has been used in criminal justice and some health settings for three decade... more Electronic monitoring has been used in criminal justice and some health settings for three decades. Technological interventions are becoming more common in psychiatry, but may be a cause for ethical concerns and controversy. We discuss electronic monitoring as an aid to security and public safety in a forensic setting.

Proceedings of the National Academy of Sciences of the United States of America, Jan 22, 2014

We present measurements of rate constants for thermal-induced reactions of the 11-cis retinyl chr... more We present measurements of rate constants for thermal-induced reactions of the 11-cis retinyl chromophore in vertebrate visual pigment rhodopsin, a process that produces noise and limits the sensitivity of vision in dim light. At temperatures of 52.0-64.6 °C, the rate constants fit well to an Arrhenius straight line with, however, an unexpectedly large activation energy of 114 ± 8 kcal/mol, which is much larger than the 60-kcal/mol photoactivation energy at 500 nm. Moreover, we obtain an unprecedentedly large prefactor of 10(72±5) s(-1), which is roughly 60 orders of magnitude larger than typical frequencies of molecular motions! At lower temperatures, the measured Arrhenius parameters become more normal: Ea = 22 ± 2 kcal/mol and Apref = 10(9±1) s(-1) in the range of 37.0-44.5 °C. We present a theoretical framework and supporting calculations that attribute this unusual temperature-dependent kinetics of rhodopsin to a lowering of the reaction barrier at higher temperatures due to en...

Optics Express, 2013

A dynamic etching approach is proposed through the appropriate variation of etchant composition r... more A dynamic etching approach is proposed through the appropriate variation of etchant composition ratio during the etching process, resulting in the parabolic shape of optical fiber nano-probe with a favorable changing of cone angle. The probe formation mechanism is thoroughly analyzed to illustrate the controllability and simplicity of this method. Optical properties of as-made probes are simulated and experimentally characterized and compared with the linear shape probes of different cone angles. It shows that the parabolic shape probes are superior to the linear shape ones with respect to the transmission efficiency and light focusing capability.

Advances in Mental Health and Intellectual Disabilities, 2012

ABSTRACT Purpose ‐ The Diagnostic Criteria for Psychiatric Disorders for Use with Adults with Lea... more ABSTRACT Purpose ‐ The Diagnostic Criteria for Psychiatric Disorders for Use with Adults with Learning Disabilities/Mental Retardation (DC-LD) was introduced in 2003 in an attempt to improve accuracy of diagnosis in the intellectual disability population. The paper aims to apply this system to a sample of a population with intellectual disability to further investigate its usefulness in the clinical setting. Design/methodology/approach ‐ A sample of 50 patients within an intellectual disability service was identified. Each individual was interviewed by a registrar in psychiatry of intellectual disability in the presence of their key worker or a carer that knew the individual well. Chart notes were extensively reviewed for clearly documented history of psychiatric symptoms and behavioural difficulties. The information gathered was applied as per the DC-LD criteria to identify appropriate diagnoses. Previously documented diagnoses were also recorded for comparison purposes. Findings ‐ There was considerable discrepancy between the rates of psychiatric diagnoses after application of DC-LD and rates of previously documented diagnoses within the sample. Use of DC-LD led to the reclassification of many previously documented diagnoses, mainly as behavioural disorders. There were also discrepancies between rates of diagnosis of pervasive developmental disorders and Alzheimer's disease before and after use of DC-LD. Originality/value ‐ This study adds to the evidence regarding the usefulness of DC-LD in the intellectual disability population and also highlights the shortcomings of non-systematic methods of diagnosis. It was agreed that DC-LD criteria be applied to all service users in this population in the future.

The Journal of Chemical Physics, 2011

A simple and efficient scheme is presented for using different time slices for different degrees ... more A simple and efficient scheme is presented for using different time slices for different degrees of freedom in path integral calculations. This method bridges the gap between full quantization and the standard mixed quantum-classical (MQC) scheme and, therefore, still provides quantum mechanical effects in the less-quantized variables. Underlying the algorithm is the notion that time slices (beads) may be "collapsed" in a manner that preserves quantization in the less quantum mechanical degrees of freedom. The method is shown to be analogous to multiple-time step integration techniques in classical molecular dynamics. The algorithm and its associated error are demonstrated on model systems containing coupled high- and low-frequency modes; results indicate that convergence of quantum mechanical observables can be achieved with disparate bead numbers in the different modes. Cost estimates indicate that this procedure, much like the MQC method, is most efficient for only a relatively few quantum mechanical degrees of freedom, such as proton transfer. In this regime, however, the cost of a fully quantum mechanical simulation is determined by the quantization of the least quantum mechanical degrees of freedom.

The Journal of Chemical Physics, 2009

We have constructed a model Hamiltonian to describe the interaction of a nitric oxide (NO) molecu... more We have constructed a model Hamiltonian to describe the interaction of a nitric oxide (NO) molecule with a Au(111) surface. The diagonal elements of the 2x2 Hamiltonian matrix represent the diabatic potential energy surfaces corresponding to the neutral and negative-ion states of the molecule. A position-dependent off-diagonal element controls the extent of mixing of the two diabatic states. The parameters of the Hamiltonian matrix were determined from ground-state density functional theory calculations, both in the absence and presence of a small applied electric field to perturb the extent of charge transfer to the molecule. The resulting model Hamiltonian satisfactorily reproduces the ab initio results, and scattering simulations of the incident translational energy dependence of trapping probability and final rotational energy of NO agree quite well with experiment. The explicit incorporation of neutral and ionic configurations should serve as a realistic and practical platform for elucidating the importance of charge transfer and nonadiabatic effects at metal surfaces, as well as provide a useful testing ground for the development of theories of nonadiabatic dynamics.

The Journal of Chemical Physics, 2011

A "tiered" appr... more A "tiered" approach to Monte Carlo sampling of nuclear configurations is presented for ab initio, self-consistent field (SCF)-based potentials, including Hartree-Fock and density functional theory. Rather than Metropolis testing only the final SCF energy, individual cycle energies are tested in a tiered fashion, without approximation. Accordingly, rejected configurations are terminated early in the SCF procedure. The method is shown to properly obey detailed balance, and effective modifications are presented for cases in which the initial SCF guess is particularly poor. Demonstrations on simple systems are provided, including an assessment of the thermal properties of the neutral water dimer with B3LYP/6-31++G**. Cost analysis indicates a factor-of-two reduction in SCF cycles, which makes the method competitive with accelerated molecular dynamics sampling techniques, without the need for forces.

Infection Control and Hospital Epidemiology, 2003

Review of health plan administrative data has been shown to be more sensitive than other methods ... more Review of health plan administrative data has been shown to be more sensitive than other methods for identifying postdischarge surgical-site infections (SSIs), but there has not been a direct comparison between this method and hospital-based surveillance for all infections, including those diagnosed before discharge. We compared these two methods for identifying SSIs following coronary artery bypass graft (CABG) procedures. We studied 1,352 CABG procedures performed among members of one health plan from March 1993 through June 1997. Health plan administrative records were reviewed based on claims containing diagnoses or procedures suggestive of infection or outpatient dispensing of antibiotics appropriate for SSI. Hospital-based surveillance information was also reviewed. SSI rates were calculated based on the total events identified by either mechanism. Postdischarge information was reviewed for 328 (85%) of 388 procedures. SSIs were confirmed in 167 patients (13% overall risk of confirmed SSI; range, 3% to 14% in the 5 hospitals). The overall sensitivity of hospital-based surveillance was 49.7% (83 of 167), and that of health plan data was 71.8% (120 of 167). There was no significant difference among hospitals in the sensitivity of either surveillance mechanism. Surveillance based on health plan data identified more postoperative infections, including those occurring before discharge, than did hospital-based surveillance. Screening administrative data and pharmacy activity may be an important adjunct to SSI surveillance, allowing efficient comparison of hospital-specific rates. Interpretation of differences among hospitals' infection rates requires case mix adjustment and understanding of variations in hospitals' discharge diagnosis coding practices.

Infection Control and Hospital Epidemiology, 2004

Nosocomial transmission of malaria is a rare phenomenon in the United States. To describe the pro... more Nosocomial transmission of malaria is a rare phenomenon in the United States. To describe the probable transmission of Plasmodium falciparum malaria from a patient to a healthcare worker and then from the healthcare worker to another patient. Case series. Two community hospitals in Massachusetts. Routine medical and supportive care. Clinical and laboratory evaluation. A nurse developed falciparum malaria after a needlestick injury from a patient with documented falciparum malaria. Three days prior to her diagnosis, she cared for another patient, who subsequently developed falciparum malaria. That patient's parasite isolate genetically matched the nurse's isolate by two independent DNA fingerprinting techniques. After extensive evaluation, we believe that a nurse who had acquired falciparum malaria via needlestick subsequently transmitted malaria to another patient via a break in standard precautions. The implications of this mechanism of transmission are discussed.

Emerging Infectious Diseases, 2004

We evaluated antimicrobial exposure, discharge diagnoses, or both to identify surgical site infec... more We evaluated antimicrobial exposure, discharge diagnoses, or both to identify surgical site infections (SSI). This retrospective cohort study in 13 hospitals involved weighted, random samples of records from 8,739 coronary artery bypass graft (CABG) procedures, 7,399 cesarean deliveries, and 6,175 breast procedures. We compared routine surveillance to detection through inpatient antimicrobial exposure (>9 days for CABG, >2 days for cesareans, and >6 days for breast procedures), discharge diagnoses, or both. Together, all methods identified SSI after 7.4% of CABG, 5.0% of cesareans, and 2.0% of breast procedures. Antimicrobial exposure had the highest sensitivity, 88%-91%, compared with routine surveillance, 38%-64%. Diagnosis codes improved sensitivity of detection of antimicrobial exposure after cesareans. Record review confirmed SSI after 31% to 38% of procedures that met antimicrobial surveillance criteria. Sufficient antimicrobial exposure days, together with diagnosis codes for cesareans, identified more postoperative SSI than routine surveillance methods. This screening method was efficient, readily standardized, and suitable for most hospitals.

Chemical Physics Letters, 2010

Polynomial extrapolation of response ('z-vector') elements is shown to reduce the cost of correla... more Polynomial extrapolation of response ('z-vector') elements is shown to reduce the cost of correlatedwavefunction, classical ab initio molecular dynamics. Demonstrations with resolution-of-the-identity Møller-Plesset perturbation theory (RI-MP2) show that the number of response equation iterations is reduced by a factor of 2-3, thereby enabling accelerated MP2 dynamics. Coupled with previously demonstrated Fock matrix extrapolation, the combined iterative SCF and z-vector calculations are reduced to a minority share of the total calculation. Though demonstrated for MP2, these methods can also be generalized to higher levels of electron correlation or excited state methods.

Chemical Physics, 2000

A combination of molecular dynamics (MD) and Monte Carlo (MC) simulation methods is proposed that... more A combination of molecular dynamics (MD) and Monte Carlo (MC) simulation methods is proposed that may have advantages in some cases over either MD or MC alone. The method is simple: in each step of the algorithm, some of the particles are moved by MC rules and the rest by MD. We prove that the mixed method converges rigorously to

Biophysical Journal, 2010

Forming upon absorption of a UV photon, excited states of DNA are subject to nonadiabatic evoluti... more Forming upon absorption of a UV photon, excited states of DNA are subject to nonadiabatic evolution, via either internal conversion (IC) back to the ground state or mutagenesis. Nonadiabatic processes following the formation of the first singlet excited states, S1, in 10 different small DNA fragmentss4 single 4′H-nucleosides, 2 Watson-Crick base pairs, and 4 nucleotide quartetsshave been investigated. Simulations were done via the nonadiabatic direct trajectory surface hopping semiclassical dynamics. The electronic wave function was obtained with configuration interaction, based on the semiempirical AM1 and PM3 Hamiltonians with fractional orbital occupation numbers. The evolution of the electronic wave function was governed by the time-dependent Schrödinger equation with a locally diabatic representation, intrinsically stable near surface crossings. The nuclei evolved on adiabatic potential energy surfaces, as prescribed by classical Newtonian dynamics, with sudden hops between potential energy surfaces to account for nonadiabatic transitions. The "fewest switches" surface hopping algorithm coupled the quantum and classical parts of the system. The dynamics simulations revealed several routes of nonadiabatic relaxation in these systems, which were not reported previously, and also recovered known routes of IC.

The American Journal of Medicine, 1981

Complications of intravenous therapy with steel needles and small-bore Teflon catheters were comp... more Complications of intravenous therapy with steel needles and small-bore Teflon catheters were compared in a randomized study of 954 cannula insertions. Cannulas were inserted and cared for by an intravenous team following a standard protocol. There were no cases of cannula-related septicemia and only one case of local infection, a cellulitis in the group in which Teflon catheters were used. There was a low incidence of positive semiquantitative cannula cultures in both treatment groups (steel needles 1.5 percent, Teflon catheters 1.4 percent). The risk of phlebitis was significantly greater with Teflon catheters (18.8 percent with Teflon catheters, 8.8 percent with steel needles, adjusted odds ratio 1.87). Steel needles were significantly associated with infiltration (17.9 percent with Teflon catheters, 40.1 percent with steel needles, adjusted odds ratio 0.39). The over-all rate of complications was significantly greater for the group in which steel needles were used (53.8 versus 64.0 percent, adjusted odds ratio 0.72), principally due to the increased risk of infiltration with steel needles. Analysis of the per day risk of infiltration and phlebitis revealed that these relationships were present for each day the cannulas remained in place. We conclude (1) that steel needles and small-bore Teflon catheters can both be used with low risk of infection and (2) that Teflon catheters more frequently cause phlebitis, whereas steel needles infiltrate more readily.

The American Journal of Medicine, 1979

Three patients with clostridial sepsis during or following hepatic arterial infusions for the reg... more Three patients with clostridial sepsis during or following hepatic arterial infusions for the regional chemotherapy of hepatic metastatic tumors are described. In all patients abdominal roentgenograms revealed lucencies in the right upper quadrant consistent with gas-containing hepatic abscesses at the time of clinically apparent sepsis and positive blood cultures. The occurrence of three such cases in one year and the low incidence of clostridial infections in non-catheterized oncology patients at our institution suggest that clostridial infection is a previously unrecognized complication of hepatic arterial infusion chemotherapy. The possible sources of the infecting organisms and pathogenesis of this infection are discussed.