相关论文: A Computational Methodology to Screen Activities o…
To directly simulate rare events using atomistic molecular dynamics is a significant challenge in computational biophysics. Well-established enhanced-sampling techniques do exist to obtain the thermodynamic functions for such systems. But…
HCN is a key ingredient for synthesizing biomolecules such as nucleobases and amino acids. We calculate 42 reaction rate coefficients directly involved with or in competition with the production of HCN in the early Earth or Titan…
Background: Nowadays, the reconstruction of genome scale metabolic models is a non-automatized and interactive process based on decision taking. This lengthy process usually requires a full year of one person's work in order to satisfactory…
We introduce a generalised micro-macro Markov chain Monte Carlo (mM-MCMC) method with pseudo-marginal approximation to the free energy, that is able to accelerate sampling of the microscopic Gibbs distributions when there is a time-scale…
A novel compute intensification methodology to the construction of low-dimensional, high-fidelity "compact" kinetic models for NOX formation is designed and demonstrated. The method adapts the data intensive Machine Learned Optimization of…
Coulomb barrier height is a basic parameter to describing the nuclear reactions. Recently it is found that ions produce from nuclear reactions can be used to study electron loss and capture processes. Hence determining the Coulomb barrier…
Background: Genome-scale metabolic network models and constraint-based modeling techniques have become important tools for analyzing cellular metabolism. Thermodynamically infeasible cy-cles (TICs) causing unbounded metabolic flux ranges…
The Fast Multipole Method (FMM) offers an acceleration for pairwise interaction calculation, known as $N$-body problems, from $\mathcal{O}(N^2)$ to $\mathcal{O}(N)$ with $N$ particles. This has brought dramatic increase in the capability of…
Recent developments in specialized computer hardware have greatly accelerated atomic level Molecular Dynamics (MD) simulations. A single GPU-attached cluster is capable of producing microsecond-length trajectories in reasonable amounts of…
Aligning theoretical atomistic structural models of materials with available experimental data presents a significant challenge for disordered systems. The configurational space to navigate is vast, and faithful realizations require large…
The integration of various types of genomic data into predictive models of biological networks is one of the main challenges currently faced by computational biology. Constraint-based models in particular play a key role in the attempt to…
Monte Carlo simulations are performed to study structure and dynamics of a protein CoVE in random media generated by a random distribution of barriers at concentration c with a coarse-grained model in its native (low temperature) and…
It has been shown that minimum free energy structure for RNAs and RNA-RNA interaction is often incorrect due to inaccuracies in the energy parameters and inherent limitations of the energy model. In contrast, ensemble based quantities such…
A family of Variational Quantum Eigensolver (VQE) methods is designed to maximize the resource of existing noisy intermediate-scale quantum (NISQ) devices. However, VQE approaches encounter various difficulties in simulating molecules of…
We show how thermodynamic properties of molecular models can be computed over a large, multidimensional parameter space by combining multistate reweighting analysis with a linear basis function approach. This approach reduces the…
Searching for potential active compounds in large databases is a necessary step to reduce time and costs in modern drug discovery pipelines. Such virtual screening methods seek to provide predictions that allow the search space to be…
The peristaltic motion of the stomach walls combines with the secretion of enzymes to initiate the process that breaks down food. Computational modelling of this phenomenon can help reveal the details that would be hard to capture via…
The step edge barrier of a prototypical organic semiconductor molecule, 3,4,9,10-perylene-tetracaboxylic-dianhydride (PTCDA) has been analysed by means of calculations based on emperical potentials. The minimum energy path (MEP) has been…
Quantum mechanics based ab-initio molecular dynamics (MD) simulation schemes offer an accurate and direct means to monitor the time-evolution of materials. Nevertheless, the expensive and repetitive energy and force computations required in…
We present an algorithm for the continuous monitoring of the biomass and ethanol concentrations and moreover the kinetic rate in the Mezcal fermentation process. This algorithm performs its task having only available the on-line…