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A recent tight-binding scheme provides a method for extending the results of first principles calculations to regimes involving $10^2 - 10^3$ atoms in a unit cell. The method uses an analytic set of two-center, non-orthogonal tight-binding…
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…
The organization of water molecules and ions between charged mineral surfaces determines the stability of colloidal suspensions and the strength of phase-separated particulate gels. In this article we assemble a density functional that…
In civil, mechanical, and aerospace engineering, structural dynamics is commonly understood to be a discipline concerned with the analysis and characterization of the vibratory response of structures. Key elements of the response are the…
The equilibrium free energy landscape of an off-lattice model protein as a function of an internal (reaction) coordinate is reconstructed from out-of-equilibrium mechanical unfolding manipulations. This task is accomplished via two…
In this work a new density functional theory framework is developed to predict the salt-concentration dependent swelling state of charged microgels and the local concentration of monovalent ions inside and outside the microgel. For this…
Solid-liquid interfaces are at the heart of many modern-day technologies and provide a challenge to many materials simulation methods. A realistic first-principles computational study of such systems entails the inclusion of solvent…
Microbial fuel cells (MFCs) perform wastewater treatment and electricity production through the conversion of organic matter using microorganisms. For practical applications, it has been suggested that greater efficiency can be achieved by…
Ensuring a satisfactory statistical convergence of anharmonic thermodynamic properties requires sampling of many atomic configurations, however the methods to obtain those necessarily produce correlated samples, thereby reducing the…
A rigorous thermodynamic treatment of partially saturated soils is developed using a minimal number of assumptions. The derivation is carried out in a way that does not require to explicitly track the complex shapes of interfaces between…
Metal coordination is ubiquitous in Nature and central in many applications ranging from nanotechnology to catalysis and environmental chemistry. Complex formation results from the subtle interplay between different thermodynamic, kinetic,…
The presence of solvent tunes many properties of a molecule, such as its ground and excited state geometry, dipole moment, excitation energy, and absorption spectrum. Because the energy of the system will vary depending on the solvent…
We address the problem of predicting the solvation free energy and equilibrium solvent density profile in fews minutes from the molecular density functional theory beyond the usual hypernetted-chain approximation. We introduce a bridge…
We introduce a novel scheme for the mechanistic investigation of solid-solid phase transitions, which we dub \textit{metashooting}. Combining transition path sampling molecular dynamics and metadynamics, this scheme allows for both a…
We report a computer simulation study of a model gel-former obtained by modifying the three-body interactions of the Stillinger-Weber potential for silicon. This modification reduces the average coordination number and consequently shifts…
To address the time-scale limitations in molecular dynamics (MD) simulations, numerous enhanced sampling methods have been developed to expedite the exploration of complex free energy landscapes. A commonly employed approach accelerates the…
Cryo-electron tomography (cryo-ET) provides a unique window into molecular organization in cellular environments (in situ). However, the interpretation of molecular structural information is complicated by several intrinsic properties of…
Understanding phononic heat transport processes in molecular junctions is a central issue in the developing field of nanoscale heat conduction and manipulation. Here we present a Stochastic Nonequlibrium Molecular Dynamics simulation…
Theoretical studies of photochemical processes require a description of the energy surfaces of excited electronic states, especially near degeneracies, where transitions between states are most likely. Systems relevant to photochemical…
In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…