Article
Chemistry, Physical
Jorge L. Rosa-Raices, Jiace Sun, Nawaf Bou-Rabee, Thomas F. Miller
Summary: Recent research highlights the importance of strong stability and dimensionality freedom for numerical integration methods in T-RPMD and path-integral molecular dynamics. The BCOCB scheme, derived from Cayley modification of the BAOAB scheme, has been shown to excel in accuracy and efficiency for configuration-dependent observables. Various integrators within a generalized class exhibit different performances for different types of quantities, with BCOCB standing out in terms of accuracy, efficiency, and stability for practical applications.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Biochemistry & Molecular Biology
Emilia P. Barros, Benjamin Ries, Lennard Boselt, Candide Champion, Sereina Riniker
Summary: Physics-based free energy simulations enable the calculation of properties in complex systems. Recent methodological advances and the introduction of machine learning approaches have improved accuracy and feasibility in multiscale modeling.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Alex Albaugh, Geyao Gu, Todd R. Gingrich
Summary: Simulations can unravel the complex relationship between molecular structure and function. In this study, we demonstrate how slight changes in a molecular motor's structure can reverse its typical dynamic behavior using molecular simulations. These findings highlight the potential of molecular simulation in guiding the development of artificial molecular motors.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Physics, Multidisciplinary
R. A. Dumer, M. Godoy
Summary: The nonequilibrium Ising model on a restricted scale-free network has been studied using Monte Carlo simulations. The dynamics of the system are defined by the probability of one- and two-spin flip processes, simulating contact with a heat bath or an external flux of energy. The study found finite critical points and calculated thermodynamic quantities and critical exponents for the system.
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Joao T. S. Coimbra, Rui P. P. Neves, Ana Cunha, Maria J. Ramos, Pedro A. Fernandes
Summary: This study investigates the influence of enzyme's dynamical flexibility on reaction mechanisms, using the first step of HIV-1 protease catalyzed reaction as a case study. The results reveal a mechanistic divergence in the enzyme, with two different reaction pathways exhibiting equivalent barriers. An active-site water molecule is suggested to play a role in influencing the mechanistic pathway.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Chemistry, Physical
Marharyta Blazhynska, Emma Goulard Coderc de Lacam, Haochuan Chen, Benoit Roux, Christophe Chipot
Summary: The study compared the rigorous geometrical route and the shortcut of omitting geometrical restraints in calculating standard binding free energies of protein-protein and protein-ligand complexes using atomistic molecular dynamics simulations. Results showed that simulations strictly following the geometrical route matched experimental measurements, while simulations without geometrical restraints converged poorly and yielded inconsistent results. This suggests the importance of including geometrical restraints for accurate calculations in molecular dynamics simulations.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Multidisciplinary Sciences
Phillip M. Rauscher, Hans Christian Ottinger, Juan J. de Pablo
Summary: Nonequilibrium interfacial thermodynamics plays a crucial role in biological, physical, and industrial-scale transport processes. In this study, we propose a theory of local equilibrium for multiphase multicomponent interfaces and use molecular dynamics simulations to validate the theory. Our results provide a thermodynamic foundation and computational tools for studying various interfacial transport phenomena.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Physics, Multidisciplinary
Silvia Pappalardi, Laura Foini, Jorge Kurchan
Summary: This letter reveals the close relationship between the eigenstate thermalization hypothesis and free probability theory, providing a mathematical framework to study quantum thermalization. This framework simplifies higher-order correlation functions and naturally incorporates the consistency property of local functions of the ETH operators.
PHYSICAL REVIEW LETTERS
(2022)
Article
Multidisciplinary Sciences
Dhiman Ray, Ly Le, Ioan Andricioaei
Summary: Researchers are focusing on the correlation between the RBD region of the SARS-CoV-2 virus and residues distant from it to understand molecular recognition events and predict key mutations for therapeutics. Their model can identify multiple residues with long-distance coupling with the RBD opening and successfully predict some key mutations.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Physics, Fluids & Plasmas
Rong-Chih Chang, An-Liang Cheng, Pik-Yin Lai
Summary: This study utilized statistical mechanics methods to investigate the growth of directed network models, with the aim of minimizing weighted connection expenses while favoring other important network properties such as weighted local node degrees. Analytic results were derived for two models, showing diverse and interesting phase transition behaviors under different weight distributions. The unexplored cases of negative node weights were also explored. The derived phase diagrams exhibited even richer phase transition behavior, including first-order transitions due to symmetry, second-order transitions with possible reentrance, and hybrid phase transitions. The developed zero-temperature simulation algorithm for undirected networks was extended to the directed case and negative node weights, allowing for efficient identification of minimal cost connection configurations. The theoretical results were verified through simulations, and possible applications and implications were discussed.
Review
Chemistry, Multidisciplinary
Ron Elber, Arman Fathizadeh, Piao Ma, Hao Wang
Summary: Time scales play a crucial role in biology, where living systems exploit variations in time scales to direct processes in desired directions. Molecular Dynamics simulations and the method of Milestoning are utilized to study dynamics of biophysical processes and enhance sampling of kinetic events, offering comprehensive pictures of complex biomolecular reactions.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2021)
Article
Chemistry, Physical
Andrea Rizzi, Paolo Carloni, Michele Parrinello
Summary: The method presented extends the theory of targeted free energy perturbation to accurately calculate free energy differences and surfaces at a quantum mechanical level from a cheaper reference potential. Accelerated convergence is achieved by increasing the overlap between target and reference distributions. The method is validated through numerical evaluations in different systems, demonstrating its effectiveness in avoiding systematic errors.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Physical
Zhaoxi Sun, Qiaole He
Summary: The combination of free energy simulations in the alchemical and configurational spaces provides a feasible route to access the thermodynamic profiles under a computationally demanding target Hamiltonian. In this work, the possibility of further accelerating the nonequilibrium free energy simulation is explored by employing unidirectional pulling and using a selection criterion. Numerical tests are performed to provide insights and guidelines for using this selection-criterion-based scheme.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Physics, Multidisciplinary
Wei-Han Li, Xiaolong Deng, Luis Santos
Summary: Study shows that in polar lattice gases, intersite interactions severely limit particle mobility and lead to fragmentation and localization of Hilbert space. Future experiments with magnetic atoms and polar molecules can explore the intriguing interplay between disorder- and interaction-induced many-body localization.
PHYSICAL REVIEW LETTERS
(2021)
Article
Chemistry, Physical
Pablo E. Videla, Victor S. Batista
Summary: An exact path-integral formalism is introduced for calculating multi-time quantum correlation functions, using canonical averages over ring-polymer dynamics in imaginary time. The formulation exploits the symmetry of path integrals with respect to permutations in imaginary time, expressing correlations as products of imaginary-time-translation-invariant phase-space functions coupled through Poisson bracket operators. The method recovers the classical limit of multi-time correlation functions and provides an interpretation of quantum dynamics in terms of interfering trajectories of the ring-polymer in phase space. The introduced phase-space formulation provides a rigorous framework for the future development of quantum dynamics methods that exploit the invariance of imaginary time path integrals to cyclic permutations.
JOURNAL OF CHEMICAL PHYSICS
(2023)
