Article
Chemistry, Multidisciplinary
Alexei Nikitin, Vladislava Milchevskaya, Alexander Lyubartsev
Summary: A more efficient version of the Expanded Ensembles method is proposed for calculating free energy in molecular-mechanical simulations. The method can achieve the same efficiency with either the optimal number of windows or a larger number compared to the original algorithm. The proposed algorithm is more robust as it allows for choosing an excess number of windows without worrying about efficiency loss.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Lisa M. Pietrek, Lukas S. Stelzl, Gerhard Hummer
Summary: Disordered proteins and nucleic acids are important in cellular function and disease. This review discusses recent advances in computationally exploring the dynamics of flexible biomolecules. While molecular dynamics simulation has improved, large-scale computing resources and validation are needed for simulating full-length disordered biopolymers. Hierarchical chain growth is a computationally efficient alternative that combines chain fragments into detailed biomolecular structures. Applications to neurodegeneration-linked proteins highlight the use of hierarchical chain growth, and connections to AI-based structural modeling are also discussed.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Article
Chemistry, Physical
Bruna F. Faria, Vladimir V. Palyulin, Aleksey M. Vishnyakov
Summary: The study focuses on the free energy and adsorption equilibrium of mobile polymer brushes, utilizing Brownian Dynamics and Expanded Ensembles Monte Carlo simulations to analyze thermodynamic properties such as excess chemical potential. Attention is given to the influence of structural features on brush height, chain radius, and in-plane radial distribution function between chain anchors.
COLLOIDS AND SURFACES A-PHYSICOCHEMICAL AND ENGINEERING ASPECTS
(2022)
Article
Chemistry, Physical
Xuda Ye, Zhennan Zhou
Summary: The study introduces an efficient sampling method for computing quantum thermal average in interacting quantum particle systems, with the potential to reduce complexity and minimize error. Numerical investigations show good convergence of the method, with a dependency of error on parameters.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Maaike M. Galama, Hao Wu, Andreas Kraemer, Mohsen Sadeghi, Frank Noe
Summary: The dynamics of molecules depend on rare event transitions between long-lived states. Enhanced sampling protocols have been introduced to efficiently explore these transitions, such as using biased or temperature-changed simulations. Two established estimators, MBAR and TRAM, are used to obtain unbiased equilibrium properties from such simulations. However, both MBAR and TRAM require iterative solving which can be time-consuming. In this study, SA is introduced to speed up the convergence of MBAR and TRAM, resulting in faster estimations without significant accuracy loss. This approach is demonstrated on various molecular systems.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Valerio Sorichetti, Andrea Ninarello, Jose Ruiz-Franco, Virginie Hugouvieux, Emanuela Zaccarelli, Cristian Micheletti, Walter Kob, Lorenzo Rovigatti
Summary: We used simulations to self-assemble polymer networks with a mixture of bivalent and tri- or tetravalent patchy particles, resulting in an exponential strand length distribution similar to experimental cross-linked systems. The fractal structure of the network depends on the assembly number density, but systems with the same mean valence and assembly density have the same structural properties. We also examined the dynamics of long strands using the tube model and found a relation between the localization lengths and shear modulus.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Engineering, Multidisciplinary
E. Prume, S. Reese, M. Ortiz
Summary: This article extends the model-free Data-Driven computing paradigm to stochastic solids and structures, inferring the likelihoods of structural outcomes of interest from empirical material data without the need for material or prior modeling. It presents an efficient method of computation and evaluation using local material data sets and admissible states.
COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING
(2023)
Article
Computer Science, Interdisciplinary Applications
Robin Fingerhut, Gabriela Guevara-Carrion, Isabel Nitzke, Denis Saric, Joshua Marx, Kai Langenbach, Sergei Prokopev, David Celny, Martin Bernreuther, Simon Stephan, Maximilian Kohns, Hans Hasse, Jadran Vrabec
Summary: The new version 4.0 of the molecular simulation tool ms2 introduces two additional potential functions and enhances computational efficiency. It also provides new properties, functionalities, and features, such as thermodynamic factor, thermal diffusion coefficients, and non-Gaussian parameters, to improve the application-oriented thermodynamic properties and microscopic structure analysis.
COMPUTER PHYSICS COMMUNICATIONS
(2021)
Article
Chemistry, Physical
Joao Morado, Paul N. Mortenson, J. Willem M. Nissink, Marcel L. Verdonk, Richard A. Ward, Jonathan W. Essex, Chris-Kriton Skylaris
Summary: Conformational analysis is crucial in drug design, and molecular mechanics simulation methods are used to generate ensembles of structures to provide reliable structural information. Reparameterizing the force field can generate FFs that closely reproduce QM results, and the MC acceptance rate is strongly correlated with various phase space overlap measurements, serving as a robust metric to evaluate the similarity between MM and QM levels of theory.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Physical
Rangsiman Ketkaew, Fabrizio Creazzo, Sandra Luber
Summary: Researchers have developed a non-instructor-led deep autoencoder neural network (DAENN) for discovering general-purpose collective variables (CVs). By training the model with unbiased trajectories that contain only reactant conformers, the network can learn molecular representations. Additionally, the introduction of topology variables and a loss-like penalty function allows for an expansion of the configurational space, improving the efficiency of CVs discovery.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
M. B. Kiataki, M. T. do N. Varella, K. Coutinho
Summary: This paper presents the application of a sequential quantum mechanics/molecular mechanics method (S-QM/MM) in computing the solvent effects on the electronic properties of solutes. The proposed self-consistent S-QM/MM polarizable electrostatic embedding (scPEE-S-QM/MM) method improves the description of solvent electron polarization and provides accurate results.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Multidisciplinary Sciences
Khetam Khasawinah, Zain Alzoubi, Abdalla Obeidat
Summary: This study estimates the surface tension, vapor density of OPC-water, and SPC/HW-heavy-water models at low temperatures using the scaled model. The free-energy difference for different molecules and a free probe is calculated using Monte Carlo simulations. The results show a linear relation between the free-energy difference and the number of molecules to the power minus one-third for n > 6. Surface tension and vapor density can be extracted from this linear relation. The critical temperature, surface tension, and vapor density are estimated for a wide range of temperatures.
Article
Materials Science, Multidisciplinary
Juan J. Alonso, B. Alles, J. G. Malherbe, V. Russier
Summary: This study investigates the magnetic order in ensembles of randomly packed magnetic spherical particles. The results show that the spatial configuration plays a crucial role in the formation of magnetic order.
Article
Chemistry, Physical
Hao Hu, Weitao Yang, Shubin Liu
Summary: We propose an efficient method to calculate the electrostatic component of solvation free energy using the two-point Pade approximation. This method only requires two simulations to determine the Pade approximant and compute the corresponding free energy contribution, making it useful for applications where accurate but computationally expensive energy functions like quantum mechanics are used. The method accurately predicts the electrostatic solvation free energy for both neutral and charged species, as demonstrated by applications to several model systems.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Review
Chemistry, Multidisciplinary
Ryan J. DiRisio, Jacob M. Finney, Anne B. McCoy
Summary: Diffusion quantum Monte Carlo (DMC) is a powerful method for obtaining the ground state energy and wave function of molecules and ions. It is particularly well suited for studying fluxional molecules and allows for easy transferability between different chemical systems. DMC calculations can be performed in Cartesian coordinates, making it a useful tool for studying nuclear quantum effects.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2022)
Article
Chemistry, Multidisciplinary
Alexei M. Nikitin
Article
Chemistry, Multidisciplinary
Alexei Nikitin, Vladislava Milchevskaya, Alexander Lyubartsev
Summary: A more efficient version of the Expanded Ensembles method is proposed for calculating free energy in molecular-mechanical simulations. The method can achieve the same efficiency with either the optimal number of windows or a larger number compared to the original algorithm. The proposed algorithm is more robust as it allows for choosing an excess number of windows without worrying about efficiency loss.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Alexei Nikitin, Vladimir Chekhov
Summary: The introduction of an additional interaction site next to nitrogen atoms greatly improves model quality with minimal impact on calculation speed. The proposed force field allows accurate prediction of heats of evaporation for compounds under investigation.
JOURNAL OF MOLECULAR MODELING
(2021)
