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We report an experimental evaluation of the "input-output surface" for a biochemical AND gate. The obtained data are modeled within the rate-equation approach, with the aim to map out the gate function and cast it in the language of logic…
A variety of natural phenomena comprises a huge number of competing reactions and short-lived intermediates. Any study of such processes requires the discovery and accurate modeling of their underlying reaction network. However, this task…
A coarse-grained computational procedure based on the Finite Element Method is proposed to calculate the normal modes and mechanical response of proteins and their supramolecular assemblies. Motivated by the elastic network model, proteins…
Our ability to calculate rates of biochemical processes using molecular dynamics simulations is severely limited by the fact that the time scales for reactions, or changes in conformational state, scale exponentially with the relevant…
Accurate determination of transition states is central to an understanding of reaction kinetics. Double-endpoint methods where both initial and final states are specified, such as the climbing image nudged elastic band (CI-NEB), identify…
Enzymes are important proteins that catalyze chemical reactions. In recent years, machine learning methods have emerged to predict enzyme function from sequence; however, there are no standardized benchmarks to evaluate these methods. We…
Discrete-state, continuous-time Markov models are becoming commonplace in the modelling of biochemical processes. The mathematical formulations that such models lead to are opaque, and, due to their complexity, are often considered…
The low-temperature driven or thermally activated motion of several condensed matter systems is often modeled by the dynamics of interfaces (co-dimension-1 elastic manifolds) subject to a random potential. Two characteristic quantitative…
Carbon-based caged and heterocyclic compounds tend to have strained molecular structures leading to high heats of formation and energetic behavior. In the current paper, molecular modelling calculations for 10 caged compounds of this type…
Activated processes from chemical reactions up to conformational transitions of large biomolecules are hampered by barriers which are overcome only by the input of some free energy of activation. Hence, the characteristic and…
We propose a novel method for the determination of the effective interaction potential between the amino acids of a protein. The strategy is based on the combination of a new optimization procedure and a geometrical argument, which also…
The recently introduced method of excess collisions (MEC) is modified to estimate diffusion-controlled reaction times inside systems of arbitrary size. The resulting MEC-E equations contain a set of empirical parameters, which have to be…
The new equimolar mixture comprises liquid crystalline compounds MHPOBC and partially fluorinated 3F2HPhF6. The phase sequence of the mixture is determined by differential scanning calorimetry, polarizing optical microscopy, X-ray…
When directly coupled with fluctuating energy sources such as wind and photovoltage power, the alkaline electrolysis (AEL) in a power-to-hydrogen (P2H) system is required to operate flexibly by dynamically adjusting its hydrogen production…
Markov chain Monte Carlo algorithms have important applications in counting problems and in machine learning problems, settings that involve estimating quantities that are difficult to compute exactly. How much can quantum computers speed…
Exploiting stochastic path integral theory, we obtain \emph{by simulation} substantial gains in efficiency for the computation of reaction rates in one-dimensional, bistable, overdamped stochastic systems. Using a well-defined measure of…
We present the Monte Carlo with Absorbing Markov Chains (MCAMC) method for extremely long kinetic Monte Carlo simulations. The MCAMC algorithm does not modify the system dynamics. It is extremely useful for models with discrete state spaces…
The evolution of molecular dynamics (MD) simulations has been intimately linked to that of computing hardware. For decades following the creation of MD, simulations have improved with computing power along the three principal dimensions of…
We present a new adaptive resolution technique for efficient particle-based multiscale molecular dynamics (MD) simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially…
The performance of quantum gate operations is experimentally determined by how correct operational parameters can be determined and set, and how stable these parameters can be maintained. In addition, gates acting on different sets of…