Article
Biochemistry & Molecular Biology
Norman Geist, Felix Nagel, Mihaela Delcea
Summary: In this study, modern replica-exchange molecular dynamics simulations were used to investigate the interaction between the ADAMTS13-MDTCS domains and the VWF-A2 domain. The findings provide comprehensive information on binding sites and interacting amino acids for each domain, revealing major binding modes. This study contributes to a better understanding of disease-related mutations and potential therapeutic improvements.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Tamas Tarjanyi, Ferenc Bogar, Janos Minarovits, Mario Gajdacs, Zsolt Toth
Summary: Titanium (Ti) is commonly used in medical and dental implants due to its tensile strength and biocompatibility. Functionalization with the tetrapeptide KRSR has been shown to promote osteoblast adhesion to implant surfaces, potentially improving bone-to implant contact and stability during healing. Computational simulations suggest that the N-terminal lysine residue in KRSR plays a crucial role in its adhesion to the TiO2 surface, influencing osseointegration of dental implants.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Lubna Ghani, Seonghoon Kim, Haoqing Wang, Hyun Sung Lee, Jonas S. Mortensen, Satoshi Katsube, Yang Du, Aiman Sadaf, Waqar Ahmed, Bernadette Byrne, Lan Guan, Claus J. Loland, Brian K. Kobilka, Wonpil Im, Pil Seok Chae
Summary: Membrane proteins are difficult to study due to limited chemical tools for stabilization. In this study, a novel detergent was developed and shown to be superior to traditional detergents in stabilizing membrane proteins. This concept of detergent foldability has potential applications in detergent design and membrane protein studies.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Geosciences, Multidisciplinary
Bingbo Gao, Ziyue Chen, YunBing Gao, Maogui Hu, Xiaolan Li, Yuchun Pan
Summary: Spatial sampling optimization is important for soil surveys and mapping. The multiple path spatial simulated annealing (MP-SSA) algorithm is developed to synchronize optimize multiobjective functions of different types and magnitudes. It outperforms other algorithms in generating the best compromised solutions.
Article
Biology
Reza Esmaeeli, Benedict Andal, Alberto Perez
Summary: This study investigates the beta subunit of E. coli DNA polymererase III, a DNA sliding clamp associated with increasing the processivity of DNA synthesis, and the opening mechanism of the clamp. Through various simulation strategies, the opening events of the sliding clamp during DNA synthesis were analyzed, and limitations in the modeling of highly charged systems with implicit solvent were noted.
Review
Endocrinology & Metabolism
Balamurugan Dhayalan, Deepak Chatterjee, Yen-Shan Chen, Michael A. Weiss
Summary: Analysis of diabetes-associated mutations in the human insulin gene has provided insights into the folding mechanisms of proinsulin, revealing the impact of mutations on pancreatic beta-cell dysfunction and insulin secretion. Studies suggest that conserved residues play a crucial role in folding efficiency and the susceptibility of proinsulin to impaired foldability can contribute to the development of diseases. This highlights the molecular links between biophysical principles and the impact on diseases such as diabetes and obesity.
FRONTIERS IN ENDOCRINOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Paola Turina, Piero Fariselli, Emidio Capriotti
Summary: The study of protein folding is crucial for understanding protein function and the relationship between genetics and phenotypes. K-Pro is a new database that collects experimental kinetic data on monomeric proteins with a two-state folding mechanism. It provides a user-friendly interface for browsing and downloading relevant data.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Arup Mondal, Alberto Perez
Summary: The MELD Bayesian approach was found to be the best performing in predicting structures from sparsely labeled NMR data, with improvements noted in an enhanced methodological pipeline. This study highlights the challenges and nature of modeling unassigned sparsely labeled NMR datasets.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Multidisciplinary Sciences
R. Charlotte Eccleston, David D. Pollock, Richard A. Goldstein
Summary: Epistasis and cooperativity in protein folding are both influenced by networks of energetic interactions within proteins, and their selection can affect each other. Selection for cooperativity may be crucial for predicting protein structure using epistasis measurements.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Tae-Eun Kim, Kotaro Tsuboyama, Scott Houliston, Cydney M. Martell, Claire M. Phoumyvong, Alexander Lemak, Hugh K. Haddox, Cheryl H. Arrowsmith, Gabriel J. Rocklin
Summary: Designing new protein structures remains challenging, and our study successfully designed stable aPPa proteins through large-scale design and test cycles, shedding light on the biophysical determinants of folding.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Computer Science, Theory & Methods
Kaixuan Feng, Zhenzhou Lu, Chunyan Ling, Lu Wang
Summary: In this paper, a fuzzy importance sampling method is proposed to improve the computational efficiency of estimating failure possibility of structures containing fuzzy uncertainty. By utilizing Markov chain simulation and adaptive kernel sampling method, a group of samples following the optimal importance sampling density is generated, leading to efficient estimation of failure possibility by using a small number of samples. The proposed method is demonstrated to be more efficient and robust compared to the original fuzzy simulation method.
FUZZY SETS AND SYSTEMS
(2021)
Article
Physics, Multidisciplinary
Aniket Rath, Rick van Bijnen, Andreas Elben, Peter Zoller, Benoit Vermersch
Summary: By combining randomized measurement protocols with importance sampling and utilizing classical techniques of machine learning and tensor networks, entanglement can be characterized in significantly larger quantum systems in a more efficient way, leading to a drastic reduction in statistical errors and required number of measurements.
PHYSICAL REVIEW LETTERS
(2021)
Review
Biochemistry & Molecular Biology
Rafayel Petrosyan, Abhishek Narayan, Michael T. Woodside
Summary: Single-molecule force spectroscopy (SMFS) is a powerful tool for studying protein folding dynamics, uncovering energy landscapes of folding, complex folding pathways, mechanisms of chaperones in assisting folding, effects of ribosomes on co-translational folding, and monitoring membrane protein folding.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Computer Science, Artificial Intelligence
Ning Wei, Zhenzhou Lu, Yingshi Hu
Summary: By introducing a Beta-hypersphere in traditional Radial-Based Importance Sampling (RBIS) method, efficiency of reliability analysis can be improved by avoiding the evaluation of Limit State Function (LSF) in safety samples located in the Beta-hypersphere. However, evaluation of LSF in safety samples outside the Beta-hypersphere is still necessary. To further enhance the efficiency, an Eccentric RBIS (ERBIS) method with an eccentric hypersphere is proposed, which can envelop more safety samples and avoid excess evaluation of LSF. The ERBIS method is demonstrated to significantly reduce LSF evaluations compared to the RBIS method.
EXPERT SYSTEMS WITH APPLICATIONS
(2023)
Article
Automation & Control Systems
Mengyu Li, Jun Yu, Tao Li, Cheng Meng
Summary: This paper introduces a novel importance sparsification method called SPAR-SINK to efficiently approximate entropy-regularized optimal transport problems. Experimental results show that SPAR-SINK outperforms mainstream competitors in terms of estimation error and speed, and it shows promising performance in echocardiogram data analysis.
JOURNAL OF MACHINE LEARNING RESEARCH
(2023)
Article
Engineering, Multidisciplinary
Salman Zarrini, Cameron F. Abrams
Summary: Understanding the structure-function relationships of the matrix-fiber interphase is crucial for enhancing the performance of composites. The complex multicomponent sizing droplets, which determine the interphase structure, are challenging to study experimentally. In this study, microsecond all-atom molecular dynamics simulations are employed to investigate the dynamics of these sizing droplets on glass fiber surfaces. The results show that the surfactant enhances wetting of the epoxy resin film former on the glass surface, while the silane coupling agent slows down the spreading by pinning the droplet via siloxyl-surface hydrogen bonding. This work contributes to a systematic understanding of the role of sizing in facilitating resin impregnation in composite lay-up.
COMPOSITES PART B-ENGINEERING
(2022)
Article
Computer Science, Interdisciplinary Applications
Zhenning Cai, Jianfeng Lu, Siyao Yang
Summary: We present fast algorithms for the summation of Dyson series and the inchworm Monte Carlo method for quantum systems coupled with harmonic baths. The algorithms are based on evolving the integro-differential equations, with the most expensive part being the computation of bath influence functionals. To accelerate the computation, we design fast algorithms that reuse the previously computed bath influence functionals, reducing the number of calculations. It is proven that these fast algorithms reduce the number of such calculations by a factor of O(N), where N is the total number of time steps. Numerical experiments are conducted to demonstrate the efficiency of the method and validate the theoretical results.
COMPUTER PHYSICS COMMUNICATIONS
(2022)
Article
Mathematics, Applied
Michael Holst, Houdong Hu, Jianfeng Lu, Jeremy L. Marzuola, Duo Song, John Weare
Summary: This paper studies symmetry breaking in the mean field solutions to the electronic structure problem for the 2 electron hydrogen molecule within the Kohn Sham (KS) local spin density functional theory with Dirac exchange. It finds that the behavior of the simplified model is related to that of the (KS) spin density functional theory predictions in condensed matter and molecular systems. The paper further analyzes and numerically computes the limiting behavior of the solutions, leading to further bifurcations and highly localized states.
JOURNAL OF NONLINEAR SCIENCE
(2022)
Article
Chemistry, Physical
Joel Bierman, Yingzhou Li, Jianfeng Lu
Summary: In this study, we propose a quantum eigensolver with an orbital optimization scheme that reduces the number of qubits required for a given problem by applying a parametrized partial unitary transformation. Through numerical simulations, we demonstrate that this method greatly enhances the capabilities of near-term quantum computers in solving electronic structure problems.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Mathematics, Applied
Zhenning Cai, Jianfeng Lu, Siyao Yang
Summary: This article focuses on the numerical analysis of the inchworm Monte Carlo method, which was recently proposed to address the numerical sign problem in open quantum systems. It is found that the inchworm Monte Carlo method demonstrates a flatter curve of numerical error growth over simulation time compared to the direct application of the Monte Carlo method to the classical Dyson series. By analyzing the inchworm Monte Carlo method, it is demonstrated that partial resummation can be utilized to balance the numerical sign problem and error amplification, effectively suppressing the former. Several numerical experiments are conducted to validate theoretical findings.
MATHEMATICS OF COMPUTATION
(2023)
Article
Computer Science, Software Engineering
Ming Huang, Cameron F. Abrams
Summary: In this work, an open-source Python package called HTPolyNet is introduced for generating realistic all-atom configurations of crosslinked polymer systems using input monomer structures and a description of the polymerization chemistry. HTPolyNet is compatible with GROMACS and General Amber Force Field, and its application to two different systems is demonstrated.
Article
Chemistry, Physical
Giulio Alberini, Sergio Alexis Paz, Beatrice Corradi, Cameron F. Abrams, Fabio Benfenati, Luca Maragliano
Summary: The cryo-EM structures of Nav channels have provided detailed information about these proteins, but our understanding of ionic permeation through the Nav pore is still limited. This study used atomistic molecular dynamics simulations to investigate the structural features of various neuronal Nav channels and revealed different mechanisms for single and double Na+ permeation through the Nav selectivity filter. The simulations also highlighted the specific configurations of ions in the filter corresponding to metastable states, providing new insights into ion conduction in Nav channels.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Mathematics, Applied
Ziang Chen, Jianfeng Lu, Yulong Lu, Shengxuan Zhou
Summary: This paper studies the regularity of solutions to the whole-space static Schrödinger equation in spectral Barron spaces. The result proves that if the source of the equation lies in the spectral Barron space I3s(Rd) and the potential function has a nonnegative lower bound decomposed into a positive constant plus a function in I3s(Rd), then the solution lies in the spectral Barron space I3s+2(Rd).
SIAM JOURNAL ON MATHEMATICAL ANALYSIS
(2023)
Article
Mathematics, Applied
Ziang Chen, Yingzhou Li, Jianfeng Lu
Summary: In this work, the authors analyze the global convergence property of a coordinate gradient descent algorithm with random choice of coordinates and stepsizes for nonconvex optimization problems. They prove that the algorithm will almost surely escape strict saddle points of the objective function under generic assumptions. The proof is based on viewing the algorithm as a nonlinear random dynamical system and analyzing its linearization around saddle points using a quantitative finite block analysis.
SIAM JOURNAL ON OPTIMIZATION
(2023)
Article
Mathematics
Min Wang, Jianfeng Lu
Summary: In this paper, neural network-based methods for solving high-dimensional quadratic porous medium equations (QPME) are proposed and studied. Three variational formulations of the nonlinear PDE are presented, including a strong formulation and two weak formulations. Extensive numerical tests are conducted to compare the pros and cons of each formulation in both low and high dimensions. This study serves as an initial exploration in solving high-dimensional nonlinear PDEs using neural network-based methods, providing useful experience for future investigations.
COMMUNICATIONS IN MATHEMATICS AND STATISTICS
(2023)
Article
Mathematics, Applied
Yu Cao, Jianfeng Lu, Lihan Wang
Summary: We provide a refined explicit estimate of the exponential decay rate of under-damped Langevin dynamics in the L-2 distance, based on a framework developed in Albritton et al. (Variational methods for the kinetic Fokker-Planck equation, arXiv arXiv:1902.04037, 2019). Our estimate provides a more explicit and simpler expression of the decay rate, and it shows a faster decay rate of O(vm) compared to m for the overdamped Langevin dynamics when the potential is convex with a Poincaré constant m << 1.
ARCHIVE FOR RATIONAL MECHANICS AND ANALYSIS
(2023)
Article
Chemistry, Physical
Zhe Wang, Zhiyuan Zhang, Jianfeng Lu, Yingzhou Li
Summary: An efficient excited state method, xCDFCI, is proposed for the computation of low-lying excited states. It extends the unconstrained nonconvex optimization problem in the CDFCI framework and incorporates coordinate descent and deterministic compression techniques.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Medicinal
Monisha Gupta, Gabriela Canziani, Charles Ang, Mohammadjavad Mohammadi, Cameron F. Abrams, Derek Yang, Amos B. Smith, Irwin Chaiken
Summary: This study aimed to verify the hypothesis that both components of the triazole Pro-Trp segment of cPTs play a role in the inactivation of the HIV-1 Env protein complex. The results showed that modifications of the Triazole Pro R group improved the binding of gp120 and cPTs, while modifications of the Trp indole side chain had disruptive effects on binding. These findings provide valuable insights for the design of HIV-1 Env inactivators.
MEDICINAL CHEMISTRY RESEARCH
(2023)
Article
Mathematics, Interdisciplinary Applications
Matthias Sachs, Deborshee Sen, Jianfeng Lu, David Dunson
Summary: Gibbs zig-zag samplers, a new class of PDMPs, update parameters in blocks using a zig-zag sampler for certain parameters and traditional MCMC-style updates for others. We demonstrate its flexibility in posterior sampling for logistic models with shrinkage priors, and provide conditions for geometric ergodicity and the validity of a central limit theorem.
Article
Physics, Mathematical
Bowen Li, Jianfeng Lu
Summary: This study introduces the quantum p-divergence and Beckner's inequalities, focusing on primitive quantum Markov semigroups on a finite-dimensional matrix algebra satisfying the detailed balance condition. The research quantifies the convergence rate of quantum dynamics, derives various implications, and computes corresponding inequalities.
JOURNAL OF STATISTICAL PHYSICS
(2023)