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, Multidisciplinary
Pengfei Tian, Adrien Lemaire, Fabien Senechal, Olivier Habrylo, Viviane Antonietti, Pascal Sonnet, Valerie Lefebvre, Frederikke Isa Marin, Robert B. Best, Jerome Pelloux, Davide Mercadante
Summary: Efficiently designing functional proteins with higher thermal stability is still challenging, especially for highly diverse sequence variants. However, optimizing sequence design based on evolutionary fitness can help improve protein stability. In this study, we used a generative evolution fitness model to design artificial sequences for a proteinaceous inhibitor of pectin methylesterase enzymes. The majority of the designs were functional, and some even showed improved thermal stability. This method has the potential to expand the sequence space of functional proteins with valuable traits for industrial applications and scientific research.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Applied
Panagiotis D. Kolokathis, Thomas Nonnen, Gerrit Fueldner, George K. Papadopoulos
Summary: A sequence of structural phases in ALPO4-5, from 4-coordinated to 6-coordinated and 5-coordinated aluminum atoms, was identified through density functional theory calculations and Rietveld refinement of XRD patterns. The thermodynamics of sorbed water at different chemical potentials were modeled using grand canonical Monte Carlo computations, explaining the hysteresis loop observed in literature isotherms during sorption-desorption cycles. Molecular dynamics simulations predicted the impact of hydrated phases on sorbate water diffusivity and calculated collective diffusivities for transport coefficients.
MICROPOROUS AND MESOPOROUS MATERIALS
(2022)
Article
Materials Science, Multidisciplinary
Carl Degitz, Manuel Konrad, Simon Kaiser, Wolfgang Wenzel
Summary: This paper compares two different modeling approaches to investigate the structure and properties of films during physical vapor deposition (PVD) process. The results show that films generated by the molecular dynamics approach have a density approximately 10% higher than those generated by the Metropolis Monte Carlo approach. Additionally, the anisotropic nature of the films is studied by calculating the refractive index, and electron and hole mobilities are calculated using a Kinetic Monte Carlo protocol.
ORGANIC ELECTRONICS
(2022)
Article
Physics, Fluids & Plasmas
Benjamin Pampel, Simon Holbach, Lisa Hartung, Omar Valsson
Summary: A common problem in computational physics and chemistry is the sampling problem, where high kinetic barriers hinder proper sampling of energy landscapes. To address this problem, many enhanced sampling methods have been developed. In a recent study, the authors introduced a novel sampling algorithm that combines overdamped Langevin dynamics with a birth-death process. In this work, the authors expand on this idea and show that the modified algorithm can efficiently sample rare event energy landscapes, regardless of the barrier height.
Article
Chemistry, Physical
Maria M. Reif, Martin Zacharias
Summary: This study presents an approach combining alchemical modifications and physical-pathway methods to calculate absolute binding free energies. It demonstrates the successful use of simultaneous alchemical transformations and physical ligand unbinding for potential of mean force calculations and nonequilibrium pulling simulations, as well as the benefits of reducing ligand-protein interactions prior to potential of mean force calculations. These methods show promise in reducing sampling problems and improving efficiency in protein-protein binding free energy calculations.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Physics, Multidisciplinary
K. L. Zhang, Z. Song
Summary: The study reveals that applying a nonlocal non-Hermitian perturbation to an Ising chain merges the topological Kramer-like degeneracy in the ferromagnetic phase, with distinct dynamic responses for different quantum phases. The phase diagram at zero temperature is completely preserved at finite temperatures.
PHYSICAL REVIEW LETTERS
(2021)
Article
Polymer Science
Filip Uhlik, Oleg V. Rud, Oleg V. Borisov, Ekaterina B. Zhulina
Summary: We present simulation results of swelling gels with comb-like or bottlebrush subchains and compare them to theory. The results confirm that the swelling coefficient of the gel increases with the polymerization degree of the main chains and exhibits a weak maximum or remains constant with the polymerization degree and grafting density of side chains. The bulk osmotic modulus shows a shallow minimum as the polymerization degree of the side chains increases, which is attributed to the overlap of side chains from different bottlebrush strands in the swollen gel.
Article
Multidisciplinary Sciences
Zhen Zhang, Jun Ding, Evan Ma
Summary: Plastic flow in metallic glasses is not caused by identifiable local defect regions. Through a realistic model, we found that shear transformations involve only a small percentage of atoms and their locations and distribution vary under different mechanical loading conditions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Physics, Multidisciplinary
Kajetan Koperwas, Marian Paluch
Summary: In this study, the dipole-dipole correlations in strongly and weakly polar model liquids were analyzed using molecular dynamics simulations. It was found that the contribution of cross-correlations to the system's total dipole moment correlation function is negligible for weakly polar liquids, but dominates over the self-correlations for strongly polar liquids.
PHYSICAL REVIEW LETTERS
(2022)
Article
Materials Science, Multidisciplinary
Jiawei Chen, Yaxin Zhu, Minsheng Huang, Lv Zhao, Shuang Liang, Shulin Yuan, Zhenhuan Li
Summary: In this study, the distribution of hydrogen around grain boundaries and the plastic response of grain boundaries under different conditions were simulated. It was found that the influence of hydrogen on dislocation nucleation from grain boundaries depends on both tensile directions and characteristics of grain boundary structures.
MATERIALS & DESIGN
(2022)
Article
Chemistry, Physical
Wei Wan, Changxin Tang, Wennan Zou
Summary: This study used a high efficient MC/MD approach to reproduce silicon [001] small angle symmetric tilt grain boundaries, focusing on the variations of grain boundary properties under different misorientation angles and the roles of dislocation stress fields in shaping special grain boundary properties. Calculations of key parameters for grain boundary structures and energies were conducted, which could benefit future grain boundary engineering.
APPLIED SURFACE SCIENCE
(2022)
Article
Nanoscience & Nanotechnology
Chang Liu, Zhen Zhang, Jun Ding, En Ma
Summary: Reverse Monte Carlo (RMC) simulations are widely used for generating three-dimensional models of amorphous materials. This study evaluates the reliability of RMC modeling for metallic glasses by comparing it with molecular dynamics simulations. The results show that RMC-generated structures lack accuracy in reproducing the local atomic packing, and additional constraints and validation check points are advised for obtaining a physically stable and meaningful atomic configuration.
SCRIPTA MATERIALIA
(2023)
Article
Mathematics, Applied
Hannes S. Vandecasteele, Giovanni Samaey
Summary: We propose a new micro-macro Markov chain Monte Carlo method to sample invariant distributions of molecular dynamics systems with time-scale separation. The algorithm allows larger proposed moves at the macroscopic level and improves exploration of the state space. We demonstrate convergence analytically, discuss the rate of convergence, and illustrate its efficiency numerically on two molecular test cases.
SIAM JOURNAL ON SCIENTIFIC COMPUTING
(2023)
Article
Computer Science, Interdisciplinary Applications
Jie Liu, Qinglin Tang, Jisheng Kou, Dingguo Xu, Tao Zhang, Shuyu Sun
Summary: Remarkable progress has been made in the application of the molecular dynamics method in engineering problems over the past two decades. However, the computational efficiency is limited due to massive-atoms system. In this study, a multi-scale molecular simulation algorithm is proposed to address this issue, and its accuracy and efficiency have been validated.
JOURNAL OF COMPUTATIONAL PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Xiaobing Li, Pierre-Andre Cazade, Pan Qi, Damien Thompson, Cunlan Guo
Summary: This study investigates the modulation of charge transport in peptide self-assembled monolayers by adjusting the position of charged residues and creating different protonation patterns. The results show that the modulation of hydrogen bonding and electrostatic interactions through pH changes affects charge transport in the peptide SAMs.
CHINESE CHEMICAL LETTERS
(2023)
Article
Chemistry, Multidisciplinary
Santi P. Rath, Damien Thompson, Sreebrata Goswami, Sreetosh Goswami
Summary: The study presents the design of temperature-resilient molecular memristors that allow for control of electronic transport by manipulating the interactions between molecules and counterions. These memristors exhibit various functionalities within a single device, and offer a deterministic design route for engineering neuromorphic devices.
ADVANCED MATERIALS
(2023)
Article
Chemistry, Physical
Bo Zhuang, Alexey Aleksandrov, Daisuke Seo, Marten H. Vos
Summary: By using ultrafast spectroscopy, it has been found that in ferredoxin-NADP+ oxidoreductase (FNR) enzymes from different sources, the photoexcited fully reduced flavin cofactor (FADred) exhibits significantly different decay rates, with Bacillus subtilis and Rhodopseudomonas palustris showing unusually fast decays and Chlorobaculum tepidum showing slower decay. This finding provides new insights into the photochemistry of fully reduced flavins and their behavior in proteins.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Multidisciplinary
Syed Abdul Ahad, Shayon Bhattacharya, Seamus Kilian, Michela Ottaviani, Kevin M. M. Ryan, Tadhg Kennedy, Damien Thompson, Hugh Geaney
Summary: Researchers have created a 3D framework of a carbon paper substrate decorated with lithiophilic nanowires to address the issues of uncontrolled dendrite formation and build-up of dead Li in Lithium (Li) metal batteries. The study shows that this design can effectively prevent dendrite formation and achieve stable cycling performance.
Article
Nanoscience & Nanotechnology
Christian A. Nijhuis, Ziyu Zhang, Francis Adoah, Cameron Nickle, Senthil Kumar Karuppannan, Lejia Wang, Li Jiang, Anton Tadich, Bruce Cowie, Teddy Salim, Dong-Chen Qi, Damien Thompson, Enrique Del Barco
Summary: This paper investigates the mechanism of charge transport across molecular wires and finds that it can be switched between the normal and Marcus Inverted regions by tuning the molecule-electrode coupling strength and the tunneling distance. The results also suggest that weak molecule-electrode coupling is important for pushing the junctions into the Marcus Inverted Region.
ADVANCED ELECTRONIC MATERIALS
(2023)
Article
Chemistry, Physical
Reabetswe R. Zwane, Joaquin Klug, Sarah Guerin, Damien Thompson, Anthony M. Reilly
Summary: In recent years, computational methods, particularly dispersion-corrected density functional theory (DFT), have been used to predict and design the mechanical response of molecular crystals. The results show that the supramolecular packing, such as extended H-bond or ir-ir networks, plays a crucial role in determining the mechanical behavior of the crystals. This has important implications for drug development.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
Article
Multidisciplinary Sciences
Poutoum P. Samire, Bo Zhuang, Bertrand Legeret, Angel Baca-Porcel, Gilles Peltier, Damien Sorigue, Alexey Aleksandrov, Frederic Beisson, Pavel Mueller
Summary: Ongoing climate change is driving the search for renewable and carbon-neutral alternatives to fossil fuels. Pho-tocatalytic conversion of fatty acids to hydrocarbons by fatty acid photodecarboxylase (FAP) represents a promising route to green fuels. Chlorella variabilis FAP (CvFAP) has higher catalytic activity on n-octanoic acid, in part, due to an autocatalytic effect of its n-heptane product.
Article
Nanoscience & Nanotechnology
Talia Bergaglio, Shayon Bhattacharya, Damien Thompson, Peter Niraj Nirmalraj
Summary: Understanding the effect of over-the-counter drugs on red blood cells is important for medical research. This study used digital holotomography to monitor the changes in red blood cells caused by ibuprofen in real-time and found that high concentrations of ibuprofen disrupt the structure and order of the red blood cell membrane.
ACS NANOSCIENCE AU
(2023)
Article
Nanoscience & Nanotechnology
Peter Niraj Nirmalraj, Marta D. Rossell, Walid Dachraoui, Damien Thompson, Michael Mayer
Summary: This study demonstrates the use of liquid-based atomic force microscope and graphene liquid-cell-based scanning transmission electron microscope to observe chemically induced protein unfolding. The results show that fully folded ferritin proteins transform into rings after urea treatment but not after guanidinium treatment. Nanorings are a specific signature of denaturation of holo-ferritins after exposure to sufficiently high urea concentrations. The study also suggests that electrostatic destabilization triggers denaturation of ferritin as urea makes direct contact with the protein and disrupts the water H-bonding network in the ferritin solvation shell.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Chemistry, Medicinal
Shubham Vishnoi, Shayon Bhattacharya, Erica M. Walsh, Grace Ilevbare Okoh, Damien Thompson
Summary: Peptides are sustainable alternatives for GPCR-linked disorders. Dual agonist peptides targeting GCGR and GLP-1R can address both diabetes and obesity, offering improved glycemic and weight loss control. In this study, optimized peptide sequences with predicted molecular binding profiles for dual agonism are designed and modeled, showing potential for future experimental testing.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Multidisciplinary
Yuehui Wang, Shuaijie Liu, Lingling Li, Hui Li, Yuanyuan Yin, Sigal Rencus-Lazar, Sarah Guerin, Wengen Ouyang, Damien Thompson, Rusen Yang, Kaiyong Cai, Ehud Gazit, Wei Ji
Summary: This study systematically explored the supramolecular engineering of amino acid-based assemblies and found that chemical modification of acetylated amino acids can enhance their piezoelectric response. By fabricating an L-AcW crystal-based piezoelectric power nanogenerator, the illumination of a light-emitting diode (LED) was successfully demonstrated using the power output of an amino acid-based piezoelectric nanogenerator.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Correction
Nanoscience & Nanotechnology
Sreetosh Goswami, Santi P. Rath, Damien Thompson, Svante Hedstrom, Meenakshi Annamalai, Rajib Pramanick, B. Robert Ilic, Soumya Sarkar, Sonu Hooda, Christian A. Nijhuis, Jens Martin, R. Stanley Williams, Sreebrata Goswami, T. Venkatesan
NATURE NANOTECHNOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Vaitea Opuu, Thomas Simonson
Summary: Enzyme design, an important application of computational protein design, can benefit from noncanonical amino acids. Genetic code expansion, achieved through engineering aminoacyl-transfer RNA synthetases, allows incorporation of over 200 noncanonical amino acids. Computational protein design can address the limitations of directed evolution and has been applied to noncanonical amino acid backbones.
PROTEIN ENGINEERING DESIGN & SELECTION
(2023)
Article
Multidisciplinary Sciences
Zhenyu Yang, Pierre-Andre Cazade, Jin-Liang Lin, Zhou Cao, Ningyue Chen, Dongdong Zhang, Lian Duan, Christian A. Nijhuis, Damien Thompson, Yuan Li
Summary: The research team has achieved fully reversible in-situ mechano-optoelectronic switching by bending the supporting electrodes to maximize aggregation-induced emission. Their study demonstrates the potential for new applications in soft electronics by optimizing the interplay between mechanical force and optics.
NATURE COMMUNICATIONS
(2023)
Article
Materials Science, Multidisciplinary
Thangavel Vijayakanth, Bin Xue, Sarah Guerin, Sigal Rencus-Lazar, Natalia Fridman, Damien Thompson, Yi Cao, Ehud Gazit
Summary: Supramolecular helical structures formed by the assembly of biological and bio-inspired building blocks have potential applications in sustainable biomedical technologies and electronics. The present study introduces a strategy to precisely formulate these structures using N-terminal protected aromatic pyridyl amino acids, which display helicity at the molecular level. The helical structure is stabilized by intermolecular hydrogen bonding. The study also demonstrates the influence of amino acid chirality on supramolecular crystal packing, self-assembly, and electromechanical properties.
JOURNAL OF MATERIALS CHEMISTRY C
(2023)