Jacek Jakowski - Academia.edu (original) (raw)
Papers by Jacek Jakowski
arXiv (Cornell University), Jul 31, 2023
ACM Transactions on Quantum Computing
We introduce QuantumGEP , a scientific computer program that uses gene expression programming (GE... more We introduce QuantumGEP , a scientific computer program that uses gene expression programming (GEP) to find a quantum circuit that either (i) maps a given set of input states to a given set of output states, or (ii) transforms a fixed initial state to minimize a given physical quantity of the output state. QuantumGEP is a driver program that uses evendim , a generic computational engine for GEP, both of which are free and open source. We apply QuantumGEP as a powerful solver for MaxCut in graphs, and for condensed matter quantum many-body Hamiltonians.
Time-dependent density functional theory (TD-DFT) is nowadays routinely applied to molecular and ... more Time-dependent density functional theory (TD-DFT) is nowadays routinely applied to molecular and nanoscaled condensed-phase materials for the calculation of electronic excitation energies and their associated optical transition probabilities. In this paper, we derive and implement expressions within the linear response TD-DFT framework for rates of transition between the ground and excited states induced by an external point charge. Symmetry considerations are given for the coupling between electronic states of well defined parity in two extreme limits of the point charge's position, and a general method to determine the range of point charge positions over which electric dipole selection rules hold for describing a given point charge induced electronic excitation is presented. The point charge induced transition rates for particular electronic excitations from linear response TD-DFT were validated through comparison to excited state populations from real time TD-DFT simulations following an impulsive 1 point charge perturbation, then evaluated on a three-dimensional grid to map their spatial dependence for a small polybenzoid. This method, when combined with information about excited state energy gradients, represents a first step toward an ab initio framework for probing the structural response of materials under electron beam irradiation due to inelastic scattering.
Journal of the American Chemical Society, Nov 27, 2003
The (TCNE)2 2dimer dianion formed by connecting two TCNEanions via a four-center, twoelectron π-o... more The (TCNE)2 2dimer dianion formed by connecting two TCNEanions via a four-center, twoelectron π-orbital bond is studied using ab initio theoretical methods and a model designed to simulate the stabilization due to surrounding counterions. (TCNE)2 2is examined as an isolated species and in a solvation environment representative of tetrahydrofuran (THF) solvent. The intrinsic strength of this novel bond and the influences of internal Coulomb repulsions, of solvent stabilization and screening, and of counterion stabilization are all considered. The geometry, electronic and thermodynamic stabilities, electronic absorption spectra, and electron detachment energies of this novel dianion are examined to help understand recent experimental findings. Our findings lead us to conclude that the (TCNE) 2 2dianion's observation in solid materials is likely a result of its stabilization by surrounding countercations. Moreover, our results suggest the dianion is geometrically metastable in THF solution, with a barrier to dissociation into two TCNEanions that can be quickly surmounted at room temperature but not at 77 K. This finding is consistent with what is observed in laboratory studies of low-and room-temperature solutions of salts containing this dianion. Finally, we assign two peaks observed (at 77 K in methyl-THF glass) in the UV-vis region to (1) electronic transitions involving the four-center orbitals and (2) detachment of an electron from the four-center π-bonding orbital to generate (TCNE) 2-+ e- .
arXiv (Cornell University), Mar 14, 2023
We introduce QuantumGEP, a scientific computer program that uses gene expression programming (GEP... more We introduce QuantumGEP, a scientific computer program that uses gene expression programming (GEP) to find a quantum circuit that either (i) maps a given set of input states to a given set of output states, or (ii) transforms a fixed initial state to minimize a given physical quantity of the output state. QuantumGEP is a driver program that uses evendim, a generic computational engine for GEP, both of which are free and open source. We apply QuantumGEP as a powerful solver for MaxCut in graphs, and for condensed matter quantum many-body Hamiltonians.
Journal of Chemical Physics, Mar 15, 2005
We have introduced a computational methodology to study vibrational spectroscopy in clusters incl... more We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantumclassical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.
Chemical Physics Letters, Feb 1, 2017
The nuclear quantum effects on the zero-point energy (ZPE), influencing adsorption of H 2 and iso... more The nuclear quantum effects on the zero-point energy (ZPE), influencing adsorption of H 2 and isotopologues on metal ions, are examined using normal mode analysis of ab initio electronic structure results for complexes with 17 metal cations. The lightest metallic nuclei, Li and Be, are found to be the most 'quantum'. The largest selectivity in adsorption is predicted for Cu, Ni and Co ions. Analysis of the nuclear wavepacket dynamics on the ground state electronic potential energy surfaces (PES) performed for complexes of Li + and Cu +2 with H 2 /D 2 /HD. shows that the PES anharmonicity changes the ZPE by up to 9%.
Journal of Chemical Theory and Computation, Nov 14, 2022
Industrial & Engineering Chemistry Research, Feb 22, 2023
arXiv (Cornell University), Jun 8, 2022
High-spatial-resolution vibrational spectroscopy is one of the principal techniques for nanoscale... more High-spatial-resolution vibrational spectroscopy is one of the principal techniques for nanoscale compositional analysis in biological materials. Here, we present a new method for the analysis of whole-cell biological specimens through nanoscale vibrational electron energy-loss spectroscopy (EELS) in the monochromated scanning transmission electron microscope. Using the combined spatial and spectral resolution of the technique, we examine the vascular system of a cucumber stem and identify clear physical and vibrational signatures from the different cellular regions with high spatial resolution. Furthermore, using first-principles calculations combined with optical and EELS spectroscopy on the individual components that make up the cucumber stem, we unravel the physical mechanisms of the vibrational signatures and directly assign compositional origins to the cell walls and bodies of different cellular regions. These results demonstrate that monochromated electron energy-loss spectroscopy is a promising technique for nanoscale spatial mapping of the chemical composition of biological materials.
Nature Communications, 2014
The attractive optoelectronic properties of conducting polymers depend sensitively upon intra- an... more The attractive optoelectronic properties of conducting polymers depend sensitively upon intra- and inter-polymer chain interactions, and therefore new methods to manipulate these interactions are continually being pursued. Here, we report a study of the isotopic effects of deuterium substitution on the structure, morphology, and optoelectronic properties of regioregular poly(3-hexylthiophene)s (P3HT) with an approach that combines the synthesis of deuterated materials, optoelectronic properties measurements, theoretical simulation, and neutron scattering. Selective substitutions of deuterium on the backbone or side-chains of P3HT result in distinct optoelectronic responses in P3HT/[6,6]-phenyl-C61-butyric acid methyl ester (PCBM) photovoltaics. Specifically, the weak non-covalent intermolecular interactions induced by the main-chain deuteration are shown to change the film crystallinity and morphology of P3HT/PCBM blends, and consequently reduce the short circuit current. However, decreased electronic coupling, the formation of a charge transfer state, and increased electron-phonon coupling resulting from side chain deuteration are shown to induce a remarkable reduction in open circuit voltage.
Time-dependent density functional theory (TD-DFT) is nowadays routinely applied to molecular and ... more Time-dependent density functional theory (TD-DFT) is nowadays routinely applied to molecular and nanoscaled condensed-phase materials for the calculation of electronic excitation energies and their associated optical transition probabilities. In this paper, we derive and implement expressions within the linear response TD-DFT framework for rates of transition between the ground and excited states induced by an external point charge. Symmetry considerations are given for the coupling between electronic states of well defined parity in two extreme limits of the point charge's position, and a general method to determine the range of point charge positions over which electric dipole selection rules hold for describing a given point charge induced electronic excitation is presented. The point charge induced transition rates for particular electronic excitations from linear response TD-DFT were validated through comparison to excited state populations from real time TD-DFT simulations following an impulsive 1 point charge perturbation, then evaluated on a three-dimensional grid to map their spatial dependence for a small polybenzoid. This method, when combined with information about excited state energy gradients, represents a first step toward an ab initio framework for probing the structural response of materials under electron beam irradiation due to inelastic scattering.
Advanced Functional Materials, Jul 1, 2017
In article number 1700749, Kai Xiao, Olga S. Ovchinnikova, and co-workers investigate a hybrid pe... more In article number 1700749, Kai Xiao, Olga S. Ovchinnikova, and co-workers investigate a hybrid perovskite films by advanced band-excitation Kelvin probe force microscopy and molecular dynamic simulations. It is revealed that incorporation of PCBM or mobile Cl-ions into the grain boundaries of the film causes suppression or enhancement of ion immigration.
Computational and Structural Biotechnology Journal
Macromolecules, 2021
Deuterium, a stable hydrogen isotope, has been playing important roles in many scientific areas, ... more Deuterium, a stable hydrogen isotope, has been playing important roles in many scientific areas, including polymer science. The developments of deuteration science and polymer science have been interwoven for the past 60 years. The unique characteristics of the scattering lengths for hydrogen isotopes (protium and deuterium) result in the dramatic differences of scattering length densities for protiated and deuterated compounds omnipresent in polymers, rendering neutron scattering a powerful tool for the investigation of polymeric structures and dynamics that are inaccessible to other tools. While the role of deuteration in neutron scattering of polymeric materials can hardly be overstated, it has also enabled the addressing of many questions using other approaches, such as NMR and vibrational spectra. In this Perspective, we provide a brief account of deuterium in the synthesis, properties, and application of various polymers. We also offer an outlook of the potentials in this ever-evolving and exciting area.
Theoretical and Computational Chemistry
Theoretical and Computational Chemistry
arXiv (Cornell University), Jul 31, 2023
ACM Transactions on Quantum Computing
We introduce QuantumGEP , a scientific computer program that uses gene expression programming (GE... more We introduce QuantumGEP , a scientific computer program that uses gene expression programming (GEP) to find a quantum circuit that either (i) maps a given set of input states to a given set of output states, or (ii) transforms a fixed initial state to minimize a given physical quantity of the output state. QuantumGEP is a driver program that uses evendim , a generic computational engine for GEP, both of which are free and open source. We apply QuantumGEP as a powerful solver for MaxCut in graphs, and for condensed matter quantum many-body Hamiltonians.
Time-dependent density functional theory (TD-DFT) is nowadays routinely applied to molecular and ... more Time-dependent density functional theory (TD-DFT) is nowadays routinely applied to molecular and nanoscaled condensed-phase materials for the calculation of electronic excitation energies and their associated optical transition probabilities. In this paper, we derive and implement expressions within the linear response TD-DFT framework for rates of transition between the ground and excited states induced by an external point charge. Symmetry considerations are given for the coupling between electronic states of well defined parity in two extreme limits of the point charge's position, and a general method to determine the range of point charge positions over which electric dipole selection rules hold for describing a given point charge induced electronic excitation is presented. The point charge induced transition rates for particular electronic excitations from linear response TD-DFT were validated through comparison to excited state populations from real time TD-DFT simulations following an impulsive 1 point charge perturbation, then evaluated on a three-dimensional grid to map their spatial dependence for a small polybenzoid. This method, when combined with information about excited state energy gradients, represents a first step toward an ab initio framework for probing the structural response of materials under electron beam irradiation due to inelastic scattering.
Journal of the American Chemical Society, Nov 27, 2003
The (TCNE)2 2dimer dianion formed by connecting two TCNEanions via a four-center, twoelectron π-o... more The (TCNE)2 2dimer dianion formed by connecting two TCNEanions via a four-center, twoelectron π-orbital bond is studied using ab initio theoretical methods and a model designed to simulate the stabilization due to surrounding counterions. (TCNE)2 2is examined as an isolated species and in a solvation environment representative of tetrahydrofuran (THF) solvent. The intrinsic strength of this novel bond and the influences of internal Coulomb repulsions, of solvent stabilization and screening, and of counterion stabilization are all considered. The geometry, electronic and thermodynamic stabilities, electronic absorption spectra, and electron detachment energies of this novel dianion are examined to help understand recent experimental findings. Our findings lead us to conclude that the (TCNE) 2 2dianion's observation in solid materials is likely a result of its stabilization by surrounding countercations. Moreover, our results suggest the dianion is geometrically metastable in THF solution, with a barrier to dissociation into two TCNEanions that can be quickly surmounted at room temperature but not at 77 K. This finding is consistent with what is observed in laboratory studies of low-and room-temperature solutions of salts containing this dianion. Finally, we assign two peaks observed (at 77 K in methyl-THF glass) in the UV-vis region to (1) electronic transitions involving the four-center orbitals and (2) detachment of an electron from the four-center π-bonding orbital to generate (TCNE) 2-+ e- .
arXiv (Cornell University), Mar 14, 2023
We introduce QuantumGEP, a scientific computer program that uses gene expression programming (GEP... more We introduce QuantumGEP, a scientific computer program that uses gene expression programming (GEP) to find a quantum circuit that either (i) maps a given set of input states to a given set of output states, or (ii) transforms a fixed initial state to minimize a given physical quantity of the output state. QuantumGEP is a driver program that uses evendim, a generic computational engine for GEP, both of which are free and open source. We apply QuantumGEP as a powerful solver for MaxCut in graphs, and for condensed matter quantum many-body Hamiltonians.
Journal of Chemical Physics, Mar 15, 2005
We have introduced a computational methodology to study vibrational spectroscopy in clusters incl... more We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantumclassical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.
Chemical Physics Letters, Feb 1, 2017
The nuclear quantum effects on the zero-point energy (ZPE), influencing adsorption of H 2 and iso... more The nuclear quantum effects on the zero-point energy (ZPE), influencing adsorption of H 2 and isotopologues on metal ions, are examined using normal mode analysis of ab initio electronic structure results for complexes with 17 metal cations. The lightest metallic nuclei, Li and Be, are found to be the most 'quantum'. The largest selectivity in adsorption is predicted for Cu, Ni and Co ions. Analysis of the nuclear wavepacket dynamics on the ground state electronic potential energy surfaces (PES) performed for complexes of Li + and Cu +2 with H 2 /D 2 /HD. shows that the PES anharmonicity changes the ZPE by up to 9%.
Journal of Chemical Theory and Computation, Nov 14, 2022
Industrial & Engineering Chemistry Research, Feb 22, 2023
arXiv (Cornell University), Jun 8, 2022
High-spatial-resolution vibrational spectroscopy is one of the principal techniques for nanoscale... more High-spatial-resolution vibrational spectroscopy is one of the principal techniques for nanoscale compositional analysis in biological materials. Here, we present a new method for the analysis of whole-cell biological specimens through nanoscale vibrational electron energy-loss spectroscopy (EELS) in the monochromated scanning transmission electron microscope. Using the combined spatial and spectral resolution of the technique, we examine the vascular system of a cucumber stem and identify clear physical and vibrational signatures from the different cellular regions with high spatial resolution. Furthermore, using first-principles calculations combined with optical and EELS spectroscopy on the individual components that make up the cucumber stem, we unravel the physical mechanisms of the vibrational signatures and directly assign compositional origins to the cell walls and bodies of different cellular regions. These results demonstrate that monochromated electron energy-loss spectroscopy is a promising technique for nanoscale spatial mapping of the chemical composition of biological materials.
Nature Communications, 2014
The attractive optoelectronic properties of conducting polymers depend sensitively upon intra- an... more The attractive optoelectronic properties of conducting polymers depend sensitively upon intra- and inter-polymer chain interactions, and therefore new methods to manipulate these interactions are continually being pursued. Here, we report a study of the isotopic effects of deuterium substitution on the structure, morphology, and optoelectronic properties of regioregular poly(3-hexylthiophene)s (P3HT) with an approach that combines the synthesis of deuterated materials, optoelectronic properties measurements, theoretical simulation, and neutron scattering. Selective substitutions of deuterium on the backbone or side-chains of P3HT result in distinct optoelectronic responses in P3HT/[6,6]-phenyl-C61-butyric acid methyl ester (PCBM) photovoltaics. Specifically, the weak non-covalent intermolecular interactions induced by the main-chain deuteration are shown to change the film crystallinity and morphology of P3HT/PCBM blends, and consequently reduce the short circuit current. However, decreased electronic coupling, the formation of a charge transfer state, and increased electron-phonon coupling resulting from side chain deuteration are shown to induce a remarkable reduction in open circuit voltage.
Time-dependent density functional theory (TD-DFT) is nowadays routinely applied to molecular and ... more Time-dependent density functional theory (TD-DFT) is nowadays routinely applied to molecular and nanoscaled condensed-phase materials for the calculation of electronic excitation energies and their associated optical transition probabilities. In this paper, we derive and implement expressions within the linear response TD-DFT framework for rates of transition between the ground and excited states induced by an external point charge. Symmetry considerations are given for the coupling between electronic states of well defined parity in two extreme limits of the point charge's position, and a general method to determine the range of point charge positions over which electric dipole selection rules hold for describing a given point charge induced electronic excitation is presented. The point charge induced transition rates for particular electronic excitations from linear response TD-DFT were validated through comparison to excited state populations from real time TD-DFT simulations following an impulsive 1 point charge perturbation, then evaluated on a three-dimensional grid to map their spatial dependence for a small polybenzoid. This method, when combined with information about excited state energy gradients, represents a first step toward an ab initio framework for probing the structural response of materials under electron beam irradiation due to inelastic scattering.
Advanced Functional Materials, Jul 1, 2017
In article number 1700749, Kai Xiao, Olga S. Ovchinnikova, and co-workers investigate a hybrid pe... more In article number 1700749, Kai Xiao, Olga S. Ovchinnikova, and co-workers investigate a hybrid perovskite films by advanced band-excitation Kelvin probe force microscopy and molecular dynamic simulations. It is revealed that incorporation of PCBM or mobile Cl-ions into the grain boundaries of the film causes suppression or enhancement of ion immigration.
Computational and Structural Biotechnology Journal
Macromolecules, 2021
Deuterium, a stable hydrogen isotope, has been playing important roles in many scientific areas, ... more Deuterium, a stable hydrogen isotope, has been playing important roles in many scientific areas, including polymer science. The developments of deuteration science and polymer science have been interwoven for the past 60 years. The unique characteristics of the scattering lengths for hydrogen isotopes (protium and deuterium) result in the dramatic differences of scattering length densities for protiated and deuterated compounds omnipresent in polymers, rendering neutron scattering a powerful tool for the investigation of polymeric structures and dynamics that are inaccessible to other tools. While the role of deuteration in neutron scattering of polymeric materials can hardly be overstated, it has also enabled the addressing of many questions using other approaches, such as NMR and vibrational spectra. In this Perspective, we provide a brief account of deuterium in the synthesis, properties, and application of various polymers. We also offer an outlook of the potentials in this ever-evolving and exciting area.
Theoretical and Computational Chemistry
Theoretical and Computational Chemistry