Related papers: Substrate-Enzyme Interaction in Pig Liver Esterase
We implement the replica exchange molecular dynamics algorithm to study the interactions of a model peptide (WALP-16) with an explicitly represented DPPC membrane bilayer. We observe the spontaneous, unbiased insertion of WALP-16 into the…
We have combined a custom implementation of the fast multiple-time-stepping LN integrator with parallel tempering to explore folding properties of small peptides in implicit solvent on the time scale of microseconds. We applied this…
All-atom molecular dynamics simulations of an elastohydrodynamic lubrication oil film are performed to study the effect of pressure. Fluid molecules of n-hexane are confined between two solid plates under a constant normal force of 0.1--8.0…
In this paper we investigate the dynamical behavior of an interface or polymer, in interaction with a distant attractive substrate. The interface is modeled by the graph of a nearest neighbor path with non-negative integer coordinates, and…
We analyse the mechanism of enzyme-substrate catalysis from the perspective of minimizing the load on the enzymes through sequestration, whilst maintaining at least a minimum reaction flux. In particular, we ask: which binding free energies…
A major challenge in electrochemistry is to decouple the reactive intermediates of a catalytic cycle to optimise their energies independently. During the oxygen evolution reaction (OER), such energy interdependence results from the need to…
Supported Lipid Bilayers (SLBs) are model membranes formed at solid substrate surfaces. This architecture renders the membrane experimentally accessible to surface sensitive techniques used to study their properties, including Atomic Force…
We present Monte Carlo simulations of liquid-crystalline material confined to a nanoscopic slit-pore. The simulations are carried out under isothermal conditions in a specialized isostress ensemble in which N fluid molecules are exposed to…
Fragmentation is an important decay mechanism for polycyclic aromatic hydrocarbons (PAHs) under harsh interstellar conditions and represents a possible formation pathway for small molecules such as H2, C2H2, C2H4. Our aim is to investigate…
The stable and metastable configurations of interstitial Mg in GaN and its migration energy barriers are studied from first-principles calculations. In addition to the conventional octahedral (O, global energy minimum) and tetrahedral (T,…
Phenalenyl is a radical nanographene with triangular shape that hosts an unpaired electron with spin S = 1/2. The open-shell nature of phenalenyl is expected to be retained in covalently bonded networks. Here, we study a first step in that…
When investigating the mode of hydrogen activation by [Fe] hydrogenases, not only the chemical reactivity at the active site is of importance but also the large-scale conformational change between the so-called open and closed…
A Density Functional study predicting a heterogeneous-catalyzed reaction giving rise to biodiesel, was performed. Triacetin was used as a model of triglyceride in the presence of an Au(111) surface as the heterogeneous catalyst substrate.…
The industrial implementation of biofuel production from lignocellulosic biomass faces a number of economic obstacles. One of these is the cost of enzymes, typically used for cellulose hydrolysis. Nature provides some hints towards the…
The kinetic analyses are quite important when it comes to understand the particle behavior in any device as they start to deviate from continuum nature. In the present study, kinetic simulations are performed using Particle-in-Cell (PIC)…
Enzyme-catalysed reactions involve two distinct timescales. There is a short timescale on which enzymes bind to substrate molecules to produce bound complexes, and a comparatively long timescale on which the complex is transformed into a…
ATPases cyclically convert chemical energy in the form of ATP gradients into directed motion inside cells. To function, ATPases rely on allosteric communication between at least two binding sites, an internal signaling mechanism that is not…
The active sites of enzymes consist of residues necessary for catalysis, and structurally important non-catalytic residues that together maintain the architecture and function of the active site. Examples of evolutionary interactions…
We study the dynamical behavior of a one dimensional interface interacting with a sticky unpenetrable substrate or wall. The interface is subject to two effects going in opposite directions. Contact between the interface and the substrate…
The surfaces of many planetary bodies, including asteroids and small moons, are covered with dust to pebble-sized regolith held weakly to the surface by gravity and contact forces. Understanding the reaction of regolith to an external…