相关论文: A Computational Methodology to Screen Activities o…
We present a semi-empirical (PM6-based) computational method for systematically estimating the effect of all possible single mutants, within a certain radius of the active site, on the barrier height of an enzymatic reaction. The intent of…
Our previously presented method for high throughput computational screening of mutant activity (Hediger et al., arXiv:1203.2950) is benchmarked against experimentally measured amidase activity for 22 mutants of Candida antarctica lipase B…
We extend the Effective Fragment Molecular Orbital (EFMO) method to the frozen domain approach where only the geometry of an active part is optimized, while the many-body polarization effects are considered for the whole system. The new…
Computational screening of naturally occurring proteins has the potential to identify efficient catalysts among the hundreds of millions of sequences that remain uncharacterized. Current experimental methods remain time, cost and labor…
Ab initio molecular dynamics (AIMD) with hybrid density functionals and plane wave basis is computationally expensive due to the high computational cost of exact exchange energy evaluation. Recently, we proposed a strategy to combine…
Computing accurate rate constants for catalytic events occurring at the surface of a given material represents a challenging task with multiple potential applications in chemistry. To address this question, we propose an approach based on a…
We analyze the efficiency of different methods for the calculation of reaction rates in the case of two simple analytical benchmark systems. Two classes of methods are considered: the first are based on the free energy calculation along a…
For the present analysis we simulate the reaction 129Xe 54+197Au79 at E=50 MeV/nucleon respectively[3]. This reaction is simulated at different impact parameters using hard equation of state. The stored phase space is then analyzed by using…
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…
An analytical formula with high accuracy is proposed for a systematic description of the capture cross sections at near-barrier energies from light to superheavy reaction systems. Based on the empirical barrier distribution (EBD) method,…
We analyze correlations in step-edge fluctuations using the Bortz-Kalos-Lebowitz kinetic Monte Carlo algorithm, with a 2-parameter expression for energy barriers, and compare with our VT-STM line-scan experiments on spiral steps on Pb(111).…
Using a reactive molecular beam with high kinetic energy ($E_{kin}$) it is possible to speed gas-surface reactions involving high activation barriers ($E_{act}$), which would require elevated pressures ($P_0$) if a random gas with a…
Atomistic rigid lattice Kinetic Monte Carlo is an efficient method for simulating nano-objects and surfaces at timescales much longer than those accessible by molecular dynamics. A laborious part of constructing any Kinetic Monte Carlo…
In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…
For ethylene carbonate on the (100) surface of lithium, we calculate the adsorption energy in two binding motifs as well as the barrier height for a ring-opening decomposition reaction. We validate a scheme for producing results in the…
The elucidation of entropic contribution to enzyme catalysis has been debated over decades. The recent experimentally measured activation enthalpy and entropy, for chorismate rearrangement reaction in PchB brings up a hotly debated issue…
Various kinetic Monte Carlo algorithms become inefficient when some of the population sizes in a system are large, which gives rise to a large number of reaction events per unit time. Here, we present a new acceleration algorithm based on…
This paper introduces a new platform to accelerate the modeling of complex aerothermochemical interactions in new turbomachines, turbo-reactors, to decarbonise chemical processes. While previous work has aerothermally demonstrated the…
The majority of therapeutic monoclonal antibodies (mAbs) on the market are produced using Chinese Hamster Ovary (CHO) cells cultured at scale in chemically defined cell culture medium. Because of the high costs associated with mammalian…
Chemical reactions are often associated with an energy barrier along the reaction pathway which hinders the spontaneity of the reaction. Changing the energy barrier along the reaction pathway allows one to modulate the performance of a…