Related papers: A Rational Method for Probing Macromolecules Disso…
Chemical separations data are typically analysed in the time domain using methods that integrate the discrete elution bands. Integrating the same chemical components across several samples must account for retention time drift over the…
The link of two concepts, indistinguishability and entanglement, with the energy-time uncertainty principle is demonstrated in a system composed of two strongly coupled bosonic modes. Working in the limit of a short interaction time, we…
We propose an ab-initio molecular dynamics method, capable to reduce dramatically the autocorrelation time required for the simulation of classical and quantum particles at finite temperature. The method is based on an efficient…
Key insights in molecular biology, such as enzyme kinetics, protein allostery and gene regulation emerged from quantitative analysis based on time-scale separation, allowing internal complexity to be eliminated and resulting in the…
We study the mechanical unfolding of a simple model protein. The Langevin dynamics results are analyzed using Markov-model methods which allow to describe completely the configurational space of the system. Using transition path theory we…
We introduce a derangement model of ligand-receptor binding that allows us to quantitatively frame the question "How can ligands seek out and bind to their optimal receptor sites in a sea of other competing ligands and suboptimal receptor…
We study the mechanics of a reversible decohesion (unzipping) of an elastic layer subjected to quasi-static end-point loading. At the micro level the system is simulated by an elastic chain of particles interacting with a rigid foundation…
Protein-ligand binding is essential to almost all life processes. The understanding of protein-ligand interactions is fundamentally important to rational drug design and protein design. Based on large scale data sets, we show that protein…
Ultracold atoms in optical lattices are versatile testbeds to study and manipulate equilibrium and out-of-equilibrium aspects of quantum many-body systems whose behavior can be described by Hubbard-type Hamiltonians. In this paper, we…
We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random…
We study DNA denaturation by integrating elasticity -- as described by the Gaussian network model -- with bond binding energies, distinguishing between different base-pair and stacking energies. We use exact calculation, within the model,…
In this contribution I critically revise the alchemical reversible approach in the context of the statistical mechanics theory of non covalent bonding in drug receptor systems. I show that most of the pitfalls and entanglements for the…
The interplay of migration, recombination, and dissociation of excitons in disordered media is studied theoretically in the low temperature regime. An exact expression for the photoluminescence spectrum is obtained. The theory is applied to…
A simple pseudo-Hamiltonian formulation is proposed for the linear inhomogeneous systems of ODEs. In contrast to the usual Hamiltonian mechanics, our approach is based on the use of non-stationary Poisson brackets, i.e. corresponding…
The spatial organization of complex biochemical reactions is essential for the regulation of cellular processes. Membrane-less structures called foci containing high concentrations of specific proteins have been reported in a variety of…
In this paper we develop an analytical model in order to study electromagnetic processes involving loosely bound neutron--rich and proton--rich nuclei. We construct a model wave function, to describe loosely bound few--body systems, having…
A new technique for the separation of macromolecules is proposed and investigated. A thin mesh with pores comparable to the radius of gyration of a free chain is used to filter chains according to their length. Without a field it has…
Understanding the kinetics of drug-protein interactions is paramount for drug design, yet the field lacks large-scale, dynamic data to move beyond static structural analysis. Here, we present DD-03B, a massively scalable database providing…
The occupation of more than one single-particle state and hence the emergence of fragmentation is a many-body phenomenon universal to systems of spatially confined interacting bosons. In the present study, we investigate the effect of the…
We introduce a method for the dissipative preparation of strongly correlated quantum states of ultracold atoms in an optical lattice via localized particle loss. The interplay of dissipation and interactions enables different types of…