Article
Biochemistry & Molecular Biology
Kim Lopez-Guell, Federica Battistini, Modesto Orozco
Summary: Traditional models of DNA flexibility, which assume local harmonic movements, fail to capture the multimodality and correlations in DNA movements. We propose a new multimodal-harmonic correlated model that provides high-quality results at a low computational cost. This model can be used to explore the dynamics of long DNA segments, approaching the chromatin range.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Seyedeh Maryam Salehi, Markus Meuwly
Summary: The changes in the dynamics of azide-labelled lysozyme compared to the wild type protein were quantitatively assessed. The location of the alanine residue affected the local and global changes in dynamics. The spectral region of the asymmetric azide stretch distinguished between alanine attachment sites.
Article
Polymer Science
Yasmin Khairy, Fernando Alvarez, Arantxa Arbe, Juan Colmenero
Summary: In this study, fully atomistic molecular dynamics simulations were conducted on polyisobutylene above the glass transition to characterize the dynamics of different kinds of atoms. All atoms, including main-chain carbons, demonstrated a crossover from Gaussian to non-Gaussian behavior in the intermediate scattering function. The research indicates that methyl-group rotations are coupled with the main-chain dynamics, challenging the assumption of the statistically independence of rotational and segmental motions.
Article
Multidisciplinary Sciences
Erik Fransson, Mattias Slabanja, Paul Erhart, Goran Wahnstrom
Summary: The perturbative treatments of lattice dynamics are limited for strongly anharmonic systems, metastable crystal structures, and liquids. Molecular dynamics simulations using correlation functions can provide access to the full dynamics of these systems, including dynamical structure factors that bridge the gap to experiment. The dynasor package is a flexible and efficient tool that simplifies the analysis of correlation functions, handling input from major MD packages and allowing for easy extension to support additional codes.
ADVANCED THEORY AND SIMULATIONS
(2021)
Article
Physics, Multidisciplinary
Nicola Molinari, Yu Xie, Ian Leifer, Aris Marcolongo, Mordechai Kornbluth, Boris Kozinsky
Summary: The method uses spectral decomposition of short-time ionic displacement covariance to accelerate computations of ionic conductivity and reduce uncertainty. It demonstrates robustness through mathematical and numerical proofs, and is applied to realistic electrolyte materials.
PHYSICAL REVIEW LETTERS
(2021)
Article
Biochemistry & Molecular Biology
Argha Mitra, Arijit Sarkar, Marton Richard Szabo, Attila Borics
Summary: Recent advancements in experimental structural biology have provided high-resolution structures of G protein-coupled receptors, shedding light on the mechanisms of transition between active and inactive states. Molecular dynamics simulations demonstrate that external stimulus transmission to the intracellular surface of the receptor involves subtle movements of polar amino acid side chains.
Article
Physics, Fluids & Plasmas
Ariana Torres-Knoop, Ivan Kryven
Summary: This work presents a data assimilation procedure for learning nonhomogeneous kinetic parameters from molecular simulations and applying them to deterministic reaction rate equations. The procedure reveals an effective differential equation for reaction kinetics, offering a new approach to predicting the long-term evolution of macroscopic systems.
Article
Multidisciplinary Sciences
Steve P. Meisburger, David A. Case, Nozomi Ando
Summary: This study presents a new experimental approach to capturing both structure and collective motions of proteins. The authors introduce two methods for robustly subtracting lattice disorder and successfully demonstrate the workflow's robustness. This work expands the capabilities of protein crystallography in interpreting diffuse scattering signals and studying protein dynamics.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Physical
Fei Zhang, Xikai Jiang, Gaofeng Chen, Yadong He, Guoqing Hu, Rui Qiao
Summary: This study investigated the electric-field-driven ion emission from the free surface of an RTIL film using molecular dynamics simulations. It found that the rate and composition of ion emission are determined by the external field and ion-surface interactions. The results provide fundamental insights to improve ion evaporation theories and enhance the performance of electrospray applications.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Physical
Taichi Inagaki, Shinji Saito
Summary: In this paper, a new hybrid method called potential scaling HMC (PS-HMC) is introduced to study complex chemical processes. By modulating the trajectory and gradually flattening the potential energy surface, the PS-HMC method is capable of constructing the canonical ensemble with a multimodal distribution. Applications to different molecular processes demonstrate the feasibility and features of this new method.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Physics, Fluids & Plasmas
Sara Pelargonio, Alessio Zaccone
Summary: We derive the Langevin equation with shear flow and its corresponding fluctuation-dissipation theorems from first principles. By starting from a classical Caldeira-Leggett Hamiltonian and modifying it with a term proportional to the strain-rate tensor, we obtain a generalized Langevin equation for the sheared system. Analytical computation of noise time-correlation functions reveals different regimes based on the intensity of the shear rate. In the limit of extremely weak shear rates compared to the effective vibrational temperature of the bath, the standard, simple, and Markovian form of the Langevin equation with shear flow postulated in the literature is valid. However, for higher shear rates, the (generalized) Langevin equation becomes non-Markovian and nontrivial fluctuation-dissipation theorems are derived.
Article
Chemistry, Physical
Dmitrii Semenok, Di Zhou, Alexander G. Kvashnin, Xiaoli Huang, Michele Galasso, Ivan A. Kruglov, Anna G. Ivanova, Alexander G. Gavriliuk, Wuhao Chen, Nikolay Tkachenko, Alexander Boldyrev, Ivan Troyan, Artem R. Oganov, Tian Cui
Summary: A joint experimental-theoretical investigation revealed novel magnetic Eu superhydrides with distinct magnetic orderings and phase transitions. The study showed that the atomic radius plays a significant role in the symmetry-breaking distortions and thermodynamic stability of superhydrides, as evidenced by close agreement between experimental data and predictions based on the DFT+U approach.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Polymer Science
Jian Li, Bokai Zhang, Yushan Li
Summary: Polymer-related materials exhibit rich glassy behaviors at different length scales due to their various molecular structures and topological constraints. Recent studies have identified transient interpenetration of long-chain rings contributing to dynamic arrest on the center-of-mass level. Interpenetration of rings is proposed as an approach to facilitate glass formation in polymer melts. Our work investigates glass transition on the nanometer-scale segments influenced by permanent interpenetration of rings using molecular dynamics simulations. We find that decreasing chain length in the mechanically interlocked system is equivalent to inducing an effective chain stiffness on the subrings, providing a unified explanation for unique structural features and transient dynamic arrest. Furthermore, our work reveals a dynamic transition from weak to strong caging at the crossover temperature, deepening the understanding of induced stiffness on glass transition.
Article
Energy & Fuels
Lin Li, Chuandong Ma, Xiaoteng Li, Jianqiao Lyu, Hao Yu, Qingbiao Wang, Zhenhua Wang, Benlu Guo, Xiaofang You
Summary: The presence of NaCl affects the viscosity of coal wastewater slurry, while the presence of CO32 hinders the adsorption of sodium lignosulfonate. HCO3 reduces the negative charge on coal particles, decreasing the apparent viscosity.
Article
Multidisciplinary Sciences
N. Gao, Z. W. Yao, G. H. Lu, H. Q. Deng, F. Gao
Summary: The study found a new diffusion mechanism for <100> interstitial dislocation loops in BCC iron using self-adaptive accelerated molecular dynamics, which represents a significant step towards understanding the mechanical behavior and microstructure evolution of the material.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Peng Teng, Geoffrey M. Gray, Mengmeng Zheng, Sylvia Singh, Xiaopeng Li, Lukasz Wojtas, Arjan van Der Vaart, Jianfeng Cai
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2019)
Article
Chemistry, Physical
Arjan van der Vaart, Paul B. Orndorff, Sang T. Le Phan
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2019)
Article
Multidisciplinary Sciences
Min Young Kim, Insung Na, Ji Sook Kim, Seung Han Son, Sungwoo Choi, Seol Eui Lee, Ji-Hun Kim, Kiseok Jang, Gil Alterovitz, Yu Chen, Arjan van der Vaart, Hyung-Sik Won, Vladimir N. Uversky, Chul Geun Kim
Article
Chemistry, Physical
Paul B. Orndorff, Sang T. Le Phan, Ka Ho Li, Arjan van der Vaart
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2020)
Article
Biochemical Research Methods
Hiqmet Kamberaj
Summary: This study combines information-and graph-theoretic measures to investigate the cluster modulation of amino acid residues and nucleotides at complex biomolecular interfaces. By introducing symbolic transfer entropy and graph-theoretic measures, it is able to identify the most influential amino acid and nucleotide sequences and reveal the modular molecular structure and binding mechanism at the interface.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2021)
Article
Parasitology
Merve Gurboga, Gizem Kugu, Hiqmet Kamberaj, Ozal Mutlu
Summary: Theileria and Babesia are eukaryotic protozoan parasites transmitted by tick vectors, causing fatal diseases in animals. Studies have shown that HDAC inhibitors have promising anti-parasitic effects. Research focusing on the HDAC1 enzyme of Babesia and Theileria species has discovered potential benzamide inhibitors.
PARASITOLOGY RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Geoffrey M. Gray, Brittany Thiessen, Arjan van der Vaart
Summary: Spider dragline silk is stored in a concentrated dope, and it is speculated to have a unique 3(1)-helical secondary structure. The spinning process and the low dielectric environment of the fiber seem to influence the formation of this structure.
BIOPHYSICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Hiqmet Kamberaj
Summary: This study employs two approaches to enhance conformational search in molecular dynamics simulations for determining transition states on a potential energy surface topology. The focus is on augmented dynamics and Tsallis statistics molecular dynamics simulations of the folding-to-unfolding transition of a peptide in a solvent environment. A dynamic graph neural networks approach is used to model dynamic information and a multi-digraph approach is suggested for determining conformation transitions. The role of water in protein denaturation is also studied, with a focus on dipole-dipole correlations and information-theoretic measures.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2022)
Article
Computer Science, Information Systems
Rabie A. Ramadan, Ahmed Y. Khedr, Kusum Yadav, Eissa Jaber Alreshidi, Md Haidar Sharif, Ahmad Taher Azar, Hiqmet Kamberaj
Summary: Cephalometric analysis is crucial for patients with dentofacial and craniofacial deformities, but manually localizing cephalometric landmarks is a time-consuming task. Therefore, a deep learning approach is proposed to automatically detect these landmarks on lateral cephalometric x-ray images. The proposed method achieves an average landmark detection rate of 90.39% to 92.37% under 2-mm and 3-mm error, respectively. Compared with state-of-the-art methods, the proposed method shows improved success in detecting landmarks under 2-mm error.
MULTIMEDIA TOOLS AND APPLICATIONS
(2022)
Article
Multidisciplinary Sciences
Paul B. Orndorff, Souvik Poddar, Aerial M. Owens, Nikita Kumari, Bryan T. Ugaz, Samrat Amin, Wade D. Van Horn, Arjan van der Vaart, Marcia Levitus
Summary: Uracil DNA-glycosylase (UNG) is an enzyme that repairs DNA by removing uracil lesions using a base flipping mechanism. The efficiency of UNG depends on the DNA sequence, with flexibility and coupling of bases around the lesion playing a major role. The finding that substrate flexibility controls UNG efficiency has implications for understanding mutation hotspot genesis, molecular evolution, and base editing.
SCIENTIFIC REPORTS
(2023)
Meeting Abstract
Biophysics
Souvik Poddar, Aerial M. Pratt, Paul B. Orndorff, Arjan van der Vaart, Wade D. Van Horn, Marcia Levitus
BIOPHYSICAL JOURNAL
(2023)
Article
Computer Science, Information Systems
Rabie A. Ramadan, Md. Haidar Sharif, Eissa Jaber Alreshidi, Md. Haris Uddin Sharif, Ibrahim Furkan Ince, Hiqmet Kamberaj, Ahmed Y. Khedr
Summary: This paper discusses the importance of fog computing in IoT applications and explores ways to optimize the placement of multi-sink nodes in fog networks to improve efficiency and energy savings. Novel solutions like the Window Nondominant Set, Evaluation Based Approach, Harris Hawks Optimizer, and Modified HHO are proposed to address challenges in fog networks. Experimental results are used to evaluate the performance of these algorithms in terms of power consumption, runtime, packet loss, and localization error.
Article
Computer Science, Artificial Intelligence
Merjem Hoxha, Hiqmet Kamberaj
Summary: This study employs a swarm artificial neural network approach to predict macromolecular properties, with molecular structures represented by feature description vectors. The aim is to develop an efficient method for training an ANN using experimental or quantum mechanics data and introducing an error model to control prediction reliability. The study utilizes four datasets, including small organic molecules, proteins with ionizable groups and mutants, and quantum mechanics calculations.
MACHINE LEARNING-SCIENCE AND TECHNOLOGY
(2021)
Review
Nanoscience & Nanotechnology
Jeffery L. Yarger, Brian R. Cherry, Arjan van der Vaart
NATURE REVIEWS MATERIALS
(2018)
Article
Computer Science, Software Engineering
Dhurata Nebiu, Hiqmet Kamberaj
