Related papers: Lipid thermodynamics : melting is molecular
Living cells use readout molecules to record the state of receptor proteins, similar to measurements or copies in typical computational devices. But is this analogy rigorous? Can cells be optimally efficient, and if not, why? We show that,…
The interfaces between metal electrodes and liquid electrolytes are prototypical in electrochemistry. That is why it is crucial to have a molecular and dynamical understating of such interfaces for both electrical properties and chemical…
Ring-polymer molecular dynamics (RPMD) has become a popular method for describing chemical reactions due to its ability to simultaneously capture tunneling, zero-point energy, anharmonicity and recrossing. Here we highlight that despite its…
It is known that lipid membranes become permeable in their melting regime. In microscopic conductance measurements on black lipid membranes one finds that conduction takes place via quantized events closely resembling those reported for…
Machine learning (ML) has emerged as a pervasive tool in science, engineering, and beyond. Its success has also led to several synergies with molecular dynamics (MD) simulations, which we use to identify and characterize the major…
Dissipative particle dynamics (DPD) is a novel particle method for mesoscale modeling of complex fluids. DPD particles are often thought to represent packets of real atoms, and the physical scale probed in DPD models are determined by the…
We propose the chemlambda artificial chemistry, whose behavior strongly suggests that real molecules which embed Interaction Nets patterns and real chemical reactions which resemble Interaction Nets graph rewrites could be a realistic path…
Classical molecular dynamics simulations of hydrogen plasmas have been performed with emphasis on the analysis of equilibration process. Theoretical basis of simulation model as well as numerically relevant aspects -- such as the proper…
A simplified interaction potential for protein folding studies at the atomic level is discussed and tested on a set of peptides with about 20 residues each. The test set contains both alpha-helical (Trp cage, Fs) and beta-sheet (GB1p,…
Molecular dynamics (MD) is a widely-used tool for simulating the molecular and materials properties. It is a common wisdom that molecular dynamics simulations should obey physical laws and, hence, lots of effort is put into ensuring that…
We review a molecular dynamics method for nucleon many-body systems called the quantum molecular dynamics (QMD) and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to the…
Nucleic acids such as mRNA have emerged as a promising therapeutic modality with the capability of addressing a wide range of diseases. Lipid nanoparticles (LNPs) as a delivery platform for nucleic acids were used in the COVID-19 vaccines…
Phase separation is the thermodynamic process that explains how droplets form in multicomponent fluids. These droplets can provide controlled compartments to localize chemical reactions, and reactions can also affect the droplets' dynamics.…
The promise of chemical computation lies in controlling systems incompatible with traditional electronic micro-controllers, with applications in synthetic biology and nano-scale manufacturing. Computation is typically embedded in…
Molecular process of polymer collapse was reproduced by isothermal molecular dynamics simulation. The initial polymer chains were obtained by mean of random walks in continuum space. Two potential models were considered to represent short…
Machine-learned interatomic potentials (MLIPs) show promise in accurately describing the physical properties of materials, but there is a need for a higher throughput method of validation. Here, we demonstrate using that MLIPs and molecular…
Molecular dynamics refers to the computer simulation of a material at the atomic level. An open problem in numerical analysis is to explain the apparent reliability of molecular dynamics simulations. The difficulty is that individual…
An approximate approach to quantum vibrational dynamics, "Brownian Chain Molecular Dynamics (BCMD)", is proposed to alleviate the chain resonance and curvature problems in the imaginary time-based path integral (PI) simulation. Here the…
Tight-binding (TB) molecular dynamics (MD) has emerged as a powerful method for investigating the atomic-scale structure of materials --- in particular the interplay between structural and electronic properties --- bridging the gap between…
Accurate prediction of a gas solubility in a liquid is crucial in many areas of chemistry, and a detailed understanding of the molecular mechanism of the gas solvation continues to be an active area of research. Here, we extend the idea of…