Related papers: Thermodynamic and Kinetic Analysis of Sensitivity …
The near-native free energy landscape of protein G is investigated through 0.4 microseconds-long atomistic molecular dynamics simulations in explicit solvent. A theoretical and computational framework is used to assess the time-dependence…
Understanding the thermodynamics of the duplication process is a fundamental step towards a comprehensive physical theory of biological systems. However, the immense complexity of real cells obscures the fundamental tensions between energy…
Living cells display a remarkable capacity to compartmentalize their functional biochemistry. A particularly fascinating example is the cell nucleus. Exchange of macromolecules between the nucleus and the surrounding cytoplasm does not…
We measure thermodynamic magnetization of a low-disordered, strongly correlated two-dimensional electron system in silicon. Pauli spin susceptibility is observed to grow critically at low electron densities - behavior that is characteristic…
We investigate the effect of vibrational degrees of freedom on the linear thermoelectric transport through a single-level quantum dot described by the spinless Anderson-Holstein impurity model. To study the effects of strong electron-phonon…
Control of the cytoskeleton and mechanical contacts with the extracellular environment are essential component of motility in eukaryotic cells. In the absence of signals, cells continuously rebuild the cytoskeleton and periodically extend…
Living cells use readout molecules to record the state of receptor proteins, similar to measurements or copies in typical computational devices. But is this analogy rigorous? Can cells be optimally efficient, and if not, why? We show that,…
Cells use temporal dynamical patterns to transmit information via signaling pathways. As optimality with respect to the environment plays a fundamental role in biological systems, organisms have evolved optimal ways to transmit information.…
Allostery refers to the puzzling phenomenon of long-range communication between distant sites in proteins. Despite its importance in biomolecular regulation and signal transduction, the underlying dynamical process is not well understood.…
The massively parallel computation of absolute binding free energy with a well-equilibrated system (MP-CAFEE) has been developed [H. Fujitani, Y. Tanida, M. Ito, G. Jayachandran, C. D. Snow, M. R. Shirts, E. J. Sorin, and V. S. Pande, J.…
High-resolution thermal-expansion and specific-heat measurements were performed on single crystalline BaFe2(As1-xPx)2 (0 < x < 0.33, x = 1). The observation of clear anomalies allows to establish the thermodynamic phase diagram which…
Cells use biochemical networks to translate environmental information into intracellular responses. These responses can be highly dynamic, but how the information is encoded in these dynamics remains poorly understood. Here we investigate…
The ultrafast dynamics of charge carriers in organic donor-acceptor interfaces are of primary importance to understanding the fundamental properties of these systems. In this work, we focus on a charge-transfer complex formed by…
Countless biological processes are fueled by energy-rich molecules like ATP and GTP that supply energy with extreme efficiency. However, designing similar energy-delivery schemes from the bottom up, essential for the development of powered…
A sensitivity analysis of general stoichiometric networks is considered. The results are presented as a generalization of Metabolic Control Analysis, which has been concerned primarily with system sensitivities at steady state. An…
Recent experiments have reported lower critical solution temperature (LCST) phase behavior of aqueous solutions of proteins induced by multivalent ions, where the solution phase separates upon heating. This phenomenon is linked to complex…
The integration time step is a critical determinant of performance in molecular dynamics simulations, governing the trade-off between speed and fidelity. Although 2 fs remains the standard in atomistic biomolecular simulations, the push for…
Magnetic particle hyperthermia, in which colloidal nanostructures are exposed to an alternating magnetic field, is a promising approach to cancer therapy. Unfortunately, the clinical efficacy of hyperthermia has not yet been optimized.…
Protein folding cooperativity is defined by the nature of the finite-size thermodynamic transition exhibited upon folding: two-state transitions show a free energy barrier between the folded and unfolded ensembles, while downhill folding is…
Folding and aggregation of proteins, the interaction between proteins and membranes, as well as the adsorption of organic soft matter to inorganic solid substrates belong to the most interesting challenges in understanding structure and…