Anubhav Jain - Academia.edu (original) (raw)
Papers by Anubhav Jain
In this work, we demonstrate a method to quantify uncertainty in corrections to density functiona... more In this work, we demonstrate a method to quantify uncertainty in corrections to density functional theory (DFT) energies based on empirical results. Such corrections are commonly used to improve the accuracy of computational enthalpies of formation, phase stability predictions, and other energy-derived properties, for example. We incorporate this method into a new DFT energy correction scheme comprising a mixture of oxidation-state and composition-dependent corrections and show that many chemical systems contain unstable polymorphs that may actually be predicted stable when uncertainty is taken into account. We then illustrate how these uncertainties can be used to estimate the probability that a compound is stable on a compositional phase diagram, thus enabling better-informed assessments of compound stability.
auto_npar option in VaspJob now properly handles Hessian calculations. WalltimeHandler now suppor... more auto_npar option in VaspJob now properly handles Hessian calculations. WalltimeHandler now supports termination at electronic step (David Waroquiers). Improved handling of BRMIX fixes.
IEEE transactions on pattern analysis and machine intelligence, 2014
Multiple kernel learning (MKL) is a principled approach for selecting and combining kernels for a... more Multiple kernel learning (MKL) is a principled approach for selecting and combining kernels for a given recognition task. A number of studies have shown that MKL is a useful tool for object recognition, where each image is represented by multiple sets of features and MKL is applied to combine different feature sets. We review the state-of-the-art for MKL, including different formulations and algorithms for solving the related optimization problems, with the focus on their applications to object recognition. One dilemma faced by practitioners interested in using MKL for object recognition is that different studies often provide conflicting results about the effectiveness and efficiency of MKL. To resolve this, we conduct extensive experiments on standard datasets to evaluate various approaches to MKL for object recognition. We argue that the seemingly contradictory conclusions offered by studies are due to different experimental setups. The conclusions of our study are: (i) given a s...
The Journal of Physical Chemistry Letters, 2015
Computational screening techniques have been found to be an effective alternative to the trial an... more Computational screening techniques have been found to be an effective alternative to the trial and error of experimentation for discovery of new materials. With increased interest in development of advanced electrical energy storage systems, it is essential to find new electrolytes that function effectively. This Perspective reviews various methods for screening electrolytes and then describes a hierarchical computational scheme to screen multiple properties of advanced electrical energy storage electrolytes using highthroughput quantum chemical calculations. The approach effectively down-selects a large pool of candidates based on successive property evaluation. As an example, results of screening are presented for redox potentials, solvation energies, and structural changes of ∼1400 organic molecules for nonaqueous redox flow batteries. Importantly, on the basis of high-throughput screening, in silico design of suitable candidate molecules for synthesis and electrochemical testing can be achieved. We anticipate that the computational approach described in this Perspective coupled with experimentation will have a significant role to play in the discovery of materials for future energy needs.
Molecular Diagnosis & Therapy, 2014
Oral cancer is one of the most commonly found cancers in many South-Asian underdeveloped countrie... more Oral cancer is one of the most commonly found cancers in many South-Asian underdeveloped countries, especially among men in comparison to women. When considering the mortality rate among all types of existing cancers, in India oral cancer is the primary reason for death in men. Some of the major reasons contributing to the high mortality rate are late diagnosis, lack of treatment options and high prevalence of tobacco consumption. Oral cancer is often diagnosed at a stage when cancer cells have already become aggressive and become resistant to standard therapeutic options. Progression, apoptosis, angiogenesis, metastasis and invasion behold great capability to treat and detect cancer at the molecular level. Dysregulation of apoptosis is one of the most common molecular events known to be associated with the development of oral cancer. In this review, we discuss key apoptotic markers which can be used as prognostic and/or therapeutic targets in oral cancer.
International journal of pharmaceutics, Jan 27, 2005
Stable polymeric microspheres capable of controlled release of tetanus toxoid (TT) for periods ra... more Stable polymeric microspheres capable of controlled release of tetanus toxoid (TT) for periods ranging from days to over months were developed. TT was stabilized, encapsulated in microspheres prepared from poly(D,L)-lactide-co-glycolide (PLGA) and chitosan by using protein stabilizer (trehalose) and its immune response was compared. The influence of co-encapsulated protein stabilizer on tetanus toxoid's stability and release from the microspheres was studied. The protein stabilizer (trehalose) prevented structural losses and aggregation of microencapsulated TT. To neutralize the acids liberated by the biodegradable lactic/glycolic acid-based polymer, we also co-incorporated into the polymer an antacid, (Mg(OH)2), which neutralized the acidity during degradation of the polymer and also prevented TT structural losses and aggregation. The in vitro release experiments with PLGA and chitosan microspheres were performed and the release of TT was increased up to 80-90%. The antigen int...
2013 Fifth International Workshop on Quality of Multimedia Experience (QoMEX), 2013
ABSTRACT
Physical Review B, 2011
Standard approximations to the density functional theory exchange-correlation functional have bee... more Standard approximations to the density functional theory exchange-correlation functional have been extraordinary successful, but calculating formation enthalpies of reactions involving compounds with both localized and delocalized electronic states remains challenging. In this work, we examine the shortcomings of the generalized gradient approximation (GGA) and GGA+U in accurately characterizing such difficult reactions. We then outline a methodology that mixes GGA and GGA+U total energies to more accurately predict formation enthalpies. We demonstrate that for a test set of 49 ternary oxides, our methodology can reduce the mean absolute relative error in calculated formation enthalpies from about 7.7-21% in GGA+U to under 2%. As another example, we show that neither GGA nor GGA+U alone accurately reproduces the Fe-P-O phase diagram; however, our mixed methodology successfully predicts all known phases as stable by naturally stitching together GGA and GGA+U results. As a final example, we demonstrate how our technique can be applied to the calculation of the Li conversion voltage of LiFeF 3. Our results indicate that mixing energies of several functionals represents one avenue to improve the accuracy of total energy computations without affecting the cost of calculation.
Journal of Applied Genetics, 2008
The ability to identify the sex of a DNA sample is an important tool in molecular ecology and con... more The ability to identify the sex of a DNA sample is an important tool in molecular ecology and conservation genetics. Control of the sex ratio is potentially of great commercial value to livestock industry, especially in the dairy and meat sector. Amplification of the SRY gene has been commonly used for sexing mammals (Lu et al. 2007). Various methods, such as cytogenetic analysis, male-specific antigen, X-linked enzyme activity, amplification based on polymerase chain reaction (PCR) of sex-specific DNA sequences (SRY gene) and X-and Y-homologous genes with indels (AMEL, UTY, or a zinc-finger gene) have been used to determine mammalian sex (Pfeiffer and Brenig 2005; Villesen and Fredsted 2006; Pomp et al. 1995). PCR-based methods are relatively simple, rapid, inexpensive and accurate (Pomp et al. 1995). Other sexing methods have the disadvantage of being time-consuming, thus delaying embryo transfer procedure. An additional disadvantage of
Electrochemistry Communications, 2010
We present an analysis of the thermal reduction of delithiated LiMnPO 4 and LiFePO 4 based on the... more We present an analysis of the thermal reduction of delithiated LiMnPO 4 and LiFePO 4 based on the quarternary phase diagrams as calculated from first principles. Our results confirm the recent experimental findings that MnPO 4 decomposes at a much lower temperature than FePO 4 , thereby potentially posing larger safety issues for LiMnPO 4 cathodes. We find that while substantial oxygen is released as MnPO 4 reduces to Mn 2 P 2 O 7 , the mixed valence phases that form in the decomposition process of FePO 4 limit the amount of oxygen evolved.
Computational Materials Science, 2011
The use of high-throughput density functional theory (DFT) calculations to screen for new materia... more The use of high-throughput density functional theory (DFT) calculations to screen for new materials and conduct fundamental research presents an exciting opportunity for materials science and materials innovation. High-throughput DFT typically involves computations on hundreds, thousands, or tens of thousands of compounds, and such a change of scale requires new calculation and data management methodologies. In this article, we describe aspects of the necessary data infrastructure for such projects to handle data generation and data analysis in a scalable way. We discuss the problem of accurately computing properties of compounds across diverse chemical spaces with a single exchange correlation functional, and demonstrate that errors in the generalized gradient approximation are highly dependent on chemical environment.
Chemistry of Materials, 2010
Finding new compounds and their crystal structures is an essential step to new materials discover... more Finding new compounds and their crystal structures is an essential step to new materials discoveries. We demonstrate how this search can be accelerated using a combination of machine learning techniques and high-throughput ab initio computations. Using a probabilistic model built on an experimental crystal structure database, novel compositions that are most likely to form a compound, and their most-probable crystal structures, are identified and tested for stability by ab initio computations. We performed such a large-scale search for new ternary oxides, discovering 209 new compounds with a limited computational budget. A list of these predicted compounds is provided, and we discuss the chemistries in which high discovery rates can be expected.
Chemistry of Materials, 2011
Cathode materials with structure similar to the mineral tavorite have shown promise for use in li... more Cathode materials with structure similar to the mineral tavorite have shown promise for use in lithium-ion batteries, but this class of materials is relatively unexplored. We use high-throughput density-functional-theory calculations to evaluate tavorite-structured oxyphosphates, fluorophosphates, oxysulfates, and fluorosulfates for use as cathode materials in lithium-ion batteries. For each material we consider the insertion of both one and two lithium ions per redox-active metal, calculating average voltages and stability relative to a database of nearly 100,000 previously-calculated compounds. To evaluate lithium mobility, we calculate the activation energies for lithium diffusion through the known tavorite cathode materials LiVO(PO 4), LiV(PO 4)F, and LiFe(SO 4)F. Our calculations indicate that tavorite-structured materials are capable of very high rates of one-dimensional lithium diffusion, and several tavorite-structured materials may be capable of reversibly inserting two lithium ions per redoxactive metal.
![Research paper thumbnail of Corrigendum to “Ab initio screening of metal sorbents for elemental mercury capture in syngas streams” [Chem. Eng. Sci. 65 (2010) 3025–3033]](https://attachments.academia-assets.com/87984548/thumbnails/1.jpg)
](Chemical Engineering Science, 2010
American Heart Journal, 1986
Chemistry of Materials, 2013
Finding new polyanionic Li-ion battery cathodes with higher capacities than LiFePO 4 is currently... more Finding new polyanionic Li-ion battery cathodes with higher capacities than LiFePO 4 is currently a major target of battery research. One approach toward this goal is to develop materials capable of exchanging more than one Li atom per transition metal. However, constraints on operating voltage due to organic electrolyte stability as well as cathode structural stability have made this target difficult to reach. More specifically, it is very challenging to develop a phosphate-based cathode in which a single element provides +2 to +4 redox activity in a reasonable voltage window: Either the voltage for the +2/+3 couple is too low (e.g., V) or the voltage for the +3/+4 couple is too high (e.g., Fe). This makes several appealing structural frameworks such as tavorites difficult to use as practical two-electron systems. Here, we propose a voltage design strategy based on the mixing of different transition metals in crystal structures known to be able to accommodate lithium in insertion and delithiation. By mixing a metal active on the +2/+3 couple (e.g., Fe) with an element active on the +3/+5 or +3/+6 couples (e.g., V or Mo), we show that high-capacity multielectron cathodes can be designed in an adequate voltage window. We illustrate our mixing strategy on LiMP 2 O 7 pyrophosphates as well as LiMPO 4 (OH) and LiM(PO 4)F tavorites, and we use density functional theory (DFT) computations to evaluate the theoretical capacity, voltage profile, and stability of the compounds proposed by our design rules. From this analysis, we identify several new compounds of potential interest as cathode materials.
In this work, we demonstrate a method to quantify uncertainty in corrections to density functiona... more In this work, we demonstrate a method to quantify uncertainty in corrections to density functional theory (DFT) energies based on empirical results. Such corrections are commonly used to improve the accuracy of computational enthalpies of formation, phase stability predictions, and other energy-derived properties, for example. We incorporate this method into a new DFT energy correction scheme comprising a mixture of oxidation-state and composition-dependent corrections and show that many chemical systems contain unstable polymorphs that may actually be predicted stable when uncertainty is taken into account. We then illustrate how these uncertainties can be used to estimate the probability that a compound is stable on a compositional phase diagram, thus enabling better-informed assessments of compound stability.
auto_npar option in VaspJob now properly handles Hessian calculations. WalltimeHandler now suppor... more auto_npar option in VaspJob now properly handles Hessian calculations. WalltimeHandler now supports termination at electronic step (David Waroquiers). Improved handling of BRMIX fixes.
IEEE transactions on pattern analysis and machine intelligence, 2014
Multiple kernel learning (MKL) is a principled approach for selecting and combining kernels for a... more Multiple kernel learning (MKL) is a principled approach for selecting and combining kernels for a given recognition task. A number of studies have shown that MKL is a useful tool for object recognition, where each image is represented by multiple sets of features and MKL is applied to combine different feature sets. We review the state-of-the-art for MKL, including different formulations and algorithms for solving the related optimization problems, with the focus on their applications to object recognition. One dilemma faced by practitioners interested in using MKL for object recognition is that different studies often provide conflicting results about the effectiveness and efficiency of MKL. To resolve this, we conduct extensive experiments on standard datasets to evaluate various approaches to MKL for object recognition. We argue that the seemingly contradictory conclusions offered by studies are due to different experimental setups. The conclusions of our study are: (i) given a s...
The Journal of Physical Chemistry Letters, 2015
Computational screening techniques have been found to be an effective alternative to the trial an... more Computational screening techniques have been found to be an effective alternative to the trial and error of experimentation for discovery of new materials. With increased interest in development of advanced electrical energy storage systems, it is essential to find new electrolytes that function effectively. This Perspective reviews various methods for screening electrolytes and then describes a hierarchical computational scheme to screen multiple properties of advanced electrical energy storage electrolytes using highthroughput quantum chemical calculations. The approach effectively down-selects a large pool of candidates based on successive property evaluation. As an example, results of screening are presented for redox potentials, solvation energies, and structural changes of ∼1400 organic molecules for nonaqueous redox flow batteries. Importantly, on the basis of high-throughput screening, in silico design of suitable candidate molecules for synthesis and electrochemical testing can be achieved. We anticipate that the computational approach described in this Perspective coupled with experimentation will have a significant role to play in the discovery of materials for future energy needs.
Molecular Diagnosis & Therapy, 2014
Oral cancer is one of the most commonly found cancers in many South-Asian underdeveloped countrie... more Oral cancer is one of the most commonly found cancers in many South-Asian underdeveloped countries, especially among men in comparison to women. When considering the mortality rate among all types of existing cancers, in India oral cancer is the primary reason for death in men. Some of the major reasons contributing to the high mortality rate are late diagnosis, lack of treatment options and high prevalence of tobacco consumption. Oral cancer is often diagnosed at a stage when cancer cells have already become aggressive and become resistant to standard therapeutic options. Progression, apoptosis, angiogenesis, metastasis and invasion behold great capability to treat and detect cancer at the molecular level. Dysregulation of apoptosis is one of the most common molecular events known to be associated with the development of oral cancer. In this review, we discuss key apoptotic markers which can be used as prognostic and/or therapeutic targets in oral cancer.
International journal of pharmaceutics, Jan 27, 2005
Stable polymeric microspheres capable of controlled release of tetanus toxoid (TT) for periods ra... more Stable polymeric microspheres capable of controlled release of tetanus toxoid (TT) for periods ranging from days to over months were developed. TT was stabilized, encapsulated in microspheres prepared from poly(D,L)-lactide-co-glycolide (PLGA) and chitosan by using protein stabilizer (trehalose) and its immune response was compared. The influence of co-encapsulated protein stabilizer on tetanus toxoid's stability and release from the microspheres was studied. The protein stabilizer (trehalose) prevented structural losses and aggregation of microencapsulated TT. To neutralize the acids liberated by the biodegradable lactic/glycolic acid-based polymer, we also co-incorporated into the polymer an antacid, (Mg(OH)2), which neutralized the acidity during degradation of the polymer and also prevented TT structural losses and aggregation. The in vitro release experiments with PLGA and chitosan microspheres were performed and the release of TT was increased up to 80-90%. The antigen int...
2013 Fifth International Workshop on Quality of Multimedia Experience (QoMEX), 2013
ABSTRACT
Physical Review B, 2011
Standard approximations to the density functional theory exchange-correlation functional have bee... more Standard approximations to the density functional theory exchange-correlation functional have been extraordinary successful, but calculating formation enthalpies of reactions involving compounds with both localized and delocalized electronic states remains challenging. In this work, we examine the shortcomings of the generalized gradient approximation (GGA) and GGA+U in accurately characterizing such difficult reactions. We then outline a methodology that mixes GGA and GGA+U total energies to more accurately predict formation enthalpies. We demonstrate that for a test set of 49 ternary oxides, our methodology can reduce the mean absolute relative error in calculated formation enthalpies from about 7.7-21% in GGA+U to under 2%. As another example, we show that neither GGA nor GGA+U alone accurately reproduces the Fe-P-O phase diagram; however, our mixed methodology successfully predicts all known phases as stable by naturally stitching together GGA and GGA+U results. As a final example, we demonstrate how our technique can be applied to the calculation of the Li conversion voltage of LiFeF 3. Our results indicate that mixing energies of several functionals represents one avenue to improve the accuracy of total energy computations without affecting the cost of calculation.
Journal of Applied Genetics, 2008
The ability to identify the sex of a DNA sample is an important tool in molecular ecology and con... more The ability to identify the sex of a DNA sample is an important tool in molecular ecology and conservation genetics. Control of the sex ratio is potentially of great commercial value to livestock industry, especially in the dairy and meat sector. Amplification of the SRY gene has been commonly used for sexing mammals (Lu et al. 2007). Various methods, such as cytogenetic analysis, male-specific antigen, X-linked enzyme activity, amplification based on polymerase chain reaction (PCR) of sex-specific DNA sequences (SRY gene) and X-and Y-homologous genes with indels (AMEL, UTY, or a zinc-finger gene) have been used to determine mammalian sex (Pfeiffer and Brenig 2005; Villesen and Fredsted 2006; Pomp et al. 1995). PCR-based methods are relatively simple, rapid, inexpensive and accurate (Pomp et al. 1995). Other sexing methods have the disadvantage of being time-consuming, thus delaying embryo transfer procedure. An additional disadvantage of
Electrochemistry Communications, 2010
We present an analysis of the thermal reduction of delithiated LiMnPO 4 and LiFePO 4 based on the... more We present an analysis of the thermal reduction of delithiated LiMnPO 4 and LiFePO 4 based on the quarternary phase diagrams as calculated from first principles. Our results confirm the recent experimental findings that MnPO 4 decomposes at a much lower temperature than FePO 4 , thereby potentially posing larger safety issues for LiMnPO 4 cathodes. We find that while substantial oxygen is released as MnPO 4 reduces to Mn 2 P 2 O 7 , the mixed valence phases that form in the decomposition process of FePO 4 limit the amount of oxygen evolved.
Computational Materials Science, 2011
The use of high-throughput density functional theory (DFT) calculations to screen for new materia... more The use of high-throughput density functional theory (DFT) calculations to screen for new materials and conduct fundamental research presents an exciting opportunity for materials science and materials innovation. High-throughput DFT typically involves computations on hundreds, thousands, or tens of thousands of compounds, and such a change of scale requires new calculation and data management methodologies. In this article, we describe aspects of the necessary data infrastructure for such projects to handle data generation and data analysis in a scalable way. We discuss the problem of accurately computing properties of compounds across diverse chemical spaces with a single exchange correlation functional, and demonstrate that errors in the generalized gradient approximation are highly dependent on chemical environment.
Chemistry of Materials, 2010
Finding new compounds and their crystal structures is an essential step to new materials discover... more Finding new compounds and their crystal structures is an essential step to new materials discoveries. We demonstrate how this search can be accelerated using a combination of machine learning techniques and high-throughput ab initio computations. Using a probabilistic model built on an experimental crystal structure database, novel compositions that are most likely to form a compound, and their most-probable crystal structures, are identified and tested for stability by ab initio computations. We performed such a large-scale search for new ternary oxides, discovering 209 new compounds with a limited computational budget. A list of these predicted compounds is provided, and we discuss the chemistries in which high discovery rates can be expected.
Chemistry of Materials, 2011
Cathode materials with structure similar to the mineral tavorite have shown promise for use in li... more Cathode materials with structure similar to the mineral tavorite have shown promise for use in lithium-ion batteries, but this class of materials is relatively unexplored. We use high-throughput density-functional-theory calculations to evaluate tavorite-structured oxyphosphates, fluorophosphates, oxysulfates, and fluorosulfates for use as cathode materials in lithium-ion batteries. For each material we consider the insertion of both one and two lithium ions per redox-active metal, calculating average voltages and stability relative to a database of nearly 100,000 previously-calculated compounds. To evaluate lithium mobility, we calculate the activation energies for lithium diffusion through the known tavorite cathode materials LiVO(PO 4), LiV(PO 4)F, and LiFe(SO 4)F. Our calculations indicate that tavorite-structured materials are capable of very high rates of one-dimensional lithium diffusion, and several tavorite-structured materials may be capable of reversibly inserting two lithium ions per redoxactive metal.
Chemical Engineering Science, 2010
American Heart Journal, 1986
Chemistry of Materials, 2013
Finding new polyanionic Li-ion battery cathodes with higher capacities than LiFePO 4 is currently... more Finding new polyanionic Li-ion battery cathodes with higher capacities than LiFePO 4 is currently a major target of battery research. One approach toward this goal is to develop materials capable of exchanging more than one Li atom per transition metal. However, constraints on operating voltage due to organic electrolyte stability as well as cathode structural stability have made this target difficult to reach. More specifically, it is very challenging to develop a phosphate-based cathode in which a single element provides +2 to +4 redox activity in a reasonable voltage window: Either the voltage for the +2/+3 couple is too low (e.g., V) or the voltage for the +3/+4 couple is too high (e.g., Fe). This makes several appealing structural frameworks such as tavorites difficult to use as practical two-electron systems. Here, we propose a voltage design strategy based on the mixing of different transition metals in crystal structures known to be able to accommodate lithium in insertion and delithiation. By mixing a metal active on the +2/+3 couple (e.g., Fe) with an element active on the +3/+5 or +3/+6 couples (e.g., V or Mo), we show that high-capacity multielectron cathodes can be designed in an adequate voltage window. We illustrate our mixing strategy on LiMP 2 O 7 pyrophosphates as well as LiMPO 4 (OH) and LiM(PO 4)F tavorites, and we use density functional theory (DFT) computations to evaluate the theoretical capacity, voltage profile, and stability of the compounds proposed by our design rules. From this analysis, we identify several new compounds of potential interest as cathode materials.