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In particular, I am interested in
Computational theory of exotic statistical ensembles and sampling methods
In particular the use of chemical potential to calculate phase related behavior requires sampling tricks. Application to systems at constant activity to explore phase transitions in saline solution and protein folding in multicomponent systems is of interest.
Forces and structures governing thermodynamics and kinetics in liquid solutions especially aqueous systems
Most difficult is the question of how multicomponent systems including cosolvents and ions affect the structure of proteins and nucleic acids in solution. Given correlations and statistical thermodynamics the relations to experimental observables on the effects ions and osmolytes have on biomacromolecules in solution should then be understandable. At the technical level we are working on activity models and diagramatic expansion.
DNA confinement
Bacteriophages, found in bacteria-rich locations like rivers and soil, are nature's machinery for viral infection of bacteria. Their genetic material, DNA or RNA, single- or double-stranded, are carried in protein-based capsids and released into the bacteria. Understanding the biophysical basis of the biological process which transfers a viral genome to infect a cell is important to the cellular machinery and many disease related fields. DNA, a charged elastic polymer, undergoes over 250-fold compaction when packed into a capsid overcoming an unfavorable thermodynamic barrier by using ATP. How DNA overcomes the unfavorable thermodynamic barrier to enter and pack inside a capsid depends on the interplay of many different intermolecular interactions. Combined with experimental data, coarse-grained models and multi-scale techniques are being employed to model the structure and, consequently, the thermodynamics of DNA confined by surfaces.
Effects of anisotropic environments on DNA and Proteins
The electric fields, solvent gradients and density waves near surfaces have profound effects on conformation and binding. Both theoretical and simulation methods are being developed to address these problems.
Theory and computational methods to investigate solution systems with couplings and correlations at many disparate length and time scales. There are many problems for which atomic correlations do not provide a direct link to macroscopic properties. Connecting meso scale averaging procedures to the atomic and macro levels via multiscale methods is important for biological/materials applications.
Computational theory of exotic statistical ensembles and sampling methods
In particular the use of chemical potential to calculate phase related behavior requires sampling tricks. Application to systems at constant activity to explore phase transitions in saline solution and protein folding in multicomponent systems is of interest.
Forces and structures governing thermodynamics and kinetics in liquid solutions especially aqueous systems
Most difficult is the question of how multicomponent systems including cosolvents and ions affect the structure of proteins and nucleic acids in solution. Given correlations and statistical thermodynamics the relations to experimental observables on the effects ions and osmolytes have on biomacromolecules in solution should then be understandable. At the technical level we are working on activity models and diagramatic expansion.
DNA confinement
Bacteriophages, found in bacteria-rich locations like rivers and soil, are nature's machinery for viral infection of bacteria. Their genetic material, DNA or RNA, single- or double-stranded, are carried in protein-based capsids and released into the bacteria. Understanding the biophysical basis of the biological process which transfers a viral genome to infect a cell is important to the cellular machinery and many disease related fields. DNA, a charged elastic polymer, undergoes over 250-fold compaction when packed into a capsid overcoming an unfavorable thermodynamic barrier by using ATP. How DNA overcomes the unfavorable thermodynamic barrier to enter and pack inside a capsid depends on the interplay of many different intermolecular interactions. Combined with experimental data, coarse-grained models and multi-scale techniques are being employed to model the structure and, consequently, the thermodynamics of DNA confined by surfaces.
Effects of anisotropic environments on DNA and Proteins
The electric fields, solvent gradients and density waves near surfaces have profound effects on conformation and binding. Both theoretical and simulation methods are being developed to address these problems.
Theory and computational methods to investigate solution systems with couplings and correlations at many disparate length and time scales. There are many problems for which atomic correlations do not provide a direct link to macroscopic properties. Connecting meso scale averaging procedures to the atomic and macro levels via multiscale methods is important for biological/materials applications.
Research Interests
Papers共 431 篇Author StatisticsCo-AuthorSimilar Experts
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Michael B Sherman,Hong Q Smith, Faith Cox, Christiane E Wobus,Gillian C Lynch,B Montgomery Pettitt,Thomas J Smith
Journal of virologypp.e0021925-e0021925, (2025)
Journal of magnetic resonance (San Diego, Calif 1997) (2025): 107890-107890
Rommie E Amaro,Johan Åqvist,Ivet Bahar,Federica Battistini, Adam Bellaiche,Daniel Beltran,Philip C Biggin,Massimiliano Bonomi,Gregory R Bowman,Richard A Bryce,Giovanni Bussi,Paolo Carloni,David A Case,Andrea Cavalli,Chia-En A Chang,Thomas E Cheatham,Margaret S Cheung,Christophe Chipot,Lillian T Chong, Preeti Choudhary,G Andres Cisneros,Cecilia Clementi,Rosana Collepardo-Guevara,Peter Coveney,Roberto Covino,T Daniel Crawford,Matteo Dal Peraro,Bert L de Groot,Lucie Delemotte,Marco De Vivo,Jonathan W Essex,Franca Fraternali,Jiali Gao,Josep Ll Gelpí,Francesco L Gervasio,Fernando D González-Nilo, Helmut Grubmüller, Marina G Guenza,Horacio V Guzman,Sarah Harris,Teresa Head-Gordon,Rigoberto Hernandez,Adam Hospital,Niu Huang,Xuhui Huang,Gerhard Hummer,Javier Iglesias-Fernández,Jan H Jensen,Shantenu Jha,Wanting Jiao,William L Jorgensen,Shina C L Kamerlin,Syma Khalid,Charles Laughton,Michael Levitt,Vittorio Limongelli,Erik Lindahl,Kresten Lindorff-Larsen, Sharon Loverde,Magnus Lundborg, Yun L Luo,F Javier Luque, Charlotte I Lynch,Alexander D MacKerell,Alessandra Magistrato,Siewert J Marrink, Hugh Martin,J Andrew McCammon,Kenneth Merz,Vicent Moliner,Adrian J Mulholland, Sohail Murad,Athi N Naganathan,Shikha Nangia,Frank Noe,Agnes Noy,Julianna Oláh,Megan L O'Mara,Mary Jo Ondrechen,Jose N Onuchic,Alexey Onufriev,Sílvia Osuna,Giulia Palermo,Anna R Panchenko,Sergio Pantano, Carol Parish,Michele Parrinello,Alberto Perez,Tomas Perez-Acle,Juan R Perilla,B Montgomery Pettitt,Adriana Pietropaolo,Jean-Philip Piquemal, Adolfo B Poma,Matej Praprotnik,Maria J Ramos,Pengyu Ren,Nathalie Reuter,Adrian Roitberg,Edina Rosta, Carme Rovira,Benoit Roux,Ursula Rothlisberger,Karissa Y Sanbonmatsu,Tamar Schlick,Alexey K Shaytan,Carlos Simmerling,Jeremy C Smith,Yuji Sugita,Katarzyna Świderek,Makoto Taiji,Peng Tao,D Peter Tieleman,Irina G Tikhonova,Julian Tirado-Rives,Iñaki Tuñón,Marc W van der Kamp,David van der Spoel,Sameer Velankar,Gregory A Voth,Rebecca Wade, Ariel Warshel,Valerie Vaissier Welborn,Stacey D Wetmore,Travis J Wheeler,Chung F Wong,Lee-Wei Yang,Martin Zacharias,Modesto Orozco
Nature methodsno. 4 (2025): 641-645
Journal of computational chemistryno. 13 (2025): e70125-e70125
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Author Statistics
#Papers: 431
#Citation: 17559
H-Index: 73
G-Index: 120
Sociability: 6
Diversity: 3
Activity: 25
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