Related papers: Computational Study of Molecular Mechanisms of Caf…
Caffeine (1,3,7-trimethylxanthine), an ingredient of coffee, is used worldwide as a psychostimulant, antioxidant, and adjuvant analgesic. To gain insights into the action mechanism of caffeine, we report on its effects on the phase…
Biological transport is supported by collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the…
Quantum computers are special purpose machines that are expected to be particularly useful in simulating strongly correlated chemical systems. The quantum computer excels at treating a moderate number of orbitals within an active space in a…
The calcium monofluoride (CaF) molecule has emerged as a promising candidate for precision measurements, quantum simulation, and ultracold chemistry experiments. Inelastic and reactive collisions of laser cooled CaF molecules in optical…
Accurate computation of non-covalent, intermolecular interaction energies is important to understand various chemical phenomena, and quantum computers are anticipated to accelerate it. Although the state-of-the-art quantum computers are…
Macromolecular complexation leading to coupling of two or more cellular membranes is a crucial step in a number of biological functions of the cell. While other mechanisms may also play a role, adhesion always involves the fluctuations of…
Studying the conformations involved in the dimerization of cadherins is highly relevant to understand the development of tissue and its failure, which is associated with tumors and metastases. Experimental techniques, like X-ray…
Finding optimal reaction coordinates and predicting accurate kinetic rates for activated processes are two of the foremost challenges of molecular simulations. We introduce an algorithm that tackles the two problems at once: starting from a…
Fundamental understanding of interatomic forces in molecules must emerge from quantum mechanics, yet widely used empirical force fields rely on simplified mechanistic approximations that often fail to capture the complexity of many-body…
We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. Within this framework it is possible to simulate on a small computer cluster reactions as complex as protein folding,…
Accurate \textit{ab initio} potential energy surfaces are essential to understand and predict collisional outcomes in ultracold molecular systems. In this study, we explore the intermolecular interactions between two laser-cooled CaF…
Coagulation and fragmentation (CF) is a fundamental process by which particles attach to each other to form clusters while existing clusters break up into smaller ones. It is a ubiquitous process that plays a key role in many physical and…
Atomic structures and adatom geometries of surfaces encode information about the thermodynamics and kinetics of the processes that lead to their formation, and which can be captured by a generative physical model. Here we develop a workflow…
Molecular dynamics (MD) simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules but are limited by the timescale barrier, i.e., we may be unable to efficiently obtain properties because we need to run…
While most work on the quantum simulation of chemistry has focused on computing energy surfaces, a similarly important application requiring subtly different algorithms is the computation of energy derivatives. Almost all molecular…
This study focuses on trying to understand the flow of argon inside carbon nanotubes. The methodology of molecular dynamics and its implementation as a tool to effectively model fluid flows inside nanocomponents is established, followed by…
A mobile manipulator often finds itself in an application where it needs to take a close-up view before performing a manipulation task. Named this as a coupled active perception and manipulation (CAPM) problem, we model the uncertainty in…
Atomic Force Microscopy (AFM) operating in the frequency modulation mode with a metal tip functionalized with a CO molecule images the internal structure of molecules with an unprecedented resolution. The interpretation of these images is…
Probing the reaction mechanisms of supramolecular processes in soft- and biological matter, such as protein aggregation, is inherently challenging. These processes emerge from the simultaneous action of multiple molecular mechanisms, each…
Machine-learned coarse-grained (CG) models have the potential for simulating large molecular complexes beyond what is possible with atomistic molecular dynamics. However, training accurate CG models remains a challenge. A widely used…