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Gene expression analysis by means of microarrays is based on the sequence specific binding of mRNA to DNA oligonucleotide probes and its measurement using fluorescent labels. The binding of RNA fragments involving other sequences than the…
DNA methylation (DNAme) is a critical component of the epigenetic regulatory machinery and aberrations in DNAme patterns occur in many diseases, such as cancer. Mapping and understanding DNAme profiles offers considerable promise for…
Parameterized artificial neural networks (ANNs) can be very expressive ansatzes for variational algorithms, reaching state-of-the-art energies on many quantum many-body Hamiltonians. Nevertheless, the training of the ANN can be slow and…
DNA-functionalized particles have great potential for the design of complex self-assembled materials. The major hurdle in realizing crystal structures from DNA-functionalized particles is expected to be kinetic barriers that trap the system…
We study settings where gradient penalties are used alongside risk minimization with the goal of obtaining predictors satisfying different notions of monotonicity. Specifically, we present two sets of contributions. In the first part of the…
An inhomogeneous helicoidal nearest-neighbor model with continuous degrees of freedom is shown to predict the same DNA melting properties as traditional long-range Ising models, for free DNA molecules in solution, as well as superhelically…
Recent advances in the understanding of the melting behavior of double-stranded DNA with statistical mechanics methods lead to improved estimates of the weight factors for the dissociation events of the chains, in particular for interior…
In this letter, we perform a sensitivity analysis on the master stability function approach for the synchronization of networks of coupled dynamical systems. More specifically, we analyze the linear stability of a nearly synchronized…
First-principles Markov Chain Monte Carlo sampling is used to investigate uncertainty quantification and uncertainty propagation in parameters describing hydrogen kinetics. Specifically, we sample the posterior distribution of thirty-one…
The Poland-Scheraga (PS) model for the helix-coil transition of DNA considers the statistical mechanics of the binding (or hybridization) of two complementary strands of DNA of equal length, with the restriction that only bases with the…
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…
The technical breakthroughs of multiple detectors developed by Daya Bay and RENO collaborations have gotten great attention. Yet the optimal determination of neutrino mixing parameters from reactor data depends on the statistical method and…
We theoretically study the molecular-weight dependence of DNA thermophoresis, which arises from mutual advection of the n repeat units of the molecular chain. As a main result we find that the dominant driving forces, i.e., the thermally…
Magnesium hydride (MgH$_2$) has been widely studied for effective hydrogen storage. However, its bulk desorption temperature (553 K) is deemed too high for practical applications. Besides doping, a strategy to decrease such reaction energy…
Cells contain multiple condensates which spontaneously form due to the heterotypic interactions between their components. Although the proteins and disordered region sequences that are responsible for condensate formation have been…
We investigate aggregation mechanism of two proteins in a thermodynamically unambiguous manner by considering the finite size effect of free energy landscape of HP lattice protein model. Multi-Self-Overlap-Ensemble Monte Carlo method is…
This paper presents a new adaptive multiscale homogenization scheme for the simulation of damage and fracture in concrete structures. A two-scale homogenization method, coupling meso-scale discrete particle models to macro- scale finite…
A method is described where the aminoacyl-tRNA synthetase system is used to create very small devices for quantitative analysis of the amino acids that occur in proteins. The basis of the method is that each of the 20 synthetases and/or a…
Circular double stranded DNA has different topological states which are defined by their linking numbers. Equilibrium distribution of linking numbers can be obtained by closing a linear DNA into a circle by ligase. Using Monte Carlo…
Superconducting phase diagram of the extended Hubbard model supplemented with interaction and hopping terms exceeding nearest neighbour distance in range is analysed systematically at different band-filling and temperature values in a…