Related papers: Free-energy landscape of polymer-crystal polymorph…
A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths --- the rare trajectories that transit between the folded and unfolded ensembles --- using only thermodynamic information, such as a…
To celebrate Hans Frauenfelder's achievements, we examine energy(-like) "landscapes" for complex living systems. Energy landscapes summarize all possible dynamics of some physical systems. Energy(-like) landscapes can explain some…
How do we search for the entire family tree without unwanted random guesses, starting from a high-index and high-energy stationary state on the energy landscape? Here we introduce a general numerical method that constructs the pathway map…
Bifurcations in kinetic pathways decide the evolution of a system. An example is crystallization, in which the thermodynamically stable polymorph may not form due to kinetic hindrance. Here, we use confined self-assembly to investigate the…
We study surface effects in amorphous polymer systems by means of computer simulation. In the framework of molecular dynamics, we present two different methods to prepare such surfaces. {\em Free} surfaces are stabilized solely by…
Protein folding is analyzed using a replica variational formalism to investigate some free energy landscape characteristics relevant for dynamics. A random contact interaction model that satisfies the minimum frustration principle is used…
We consider the crystallization problem for a finite one-dimensional collection of identical hard spheres in a periodic energy landscape. This issue arises in connection with the investigation of crystalline states of ionic dimers, as well…
Granular materials such as sand, powders, and food grains are ubiquitous in civil engineering, geoscience, agriculture, and medicine. While the influence of friction between the grains on the static structure of these systems is well…
High-dimensional random landscapes underlie phenomena as diverse as glassy physics and optimization in machine learning, and even their simplest toy models already display extraordinarily rich behavior. This thesis aims to deepen our…
Translating the complex, multi-dimensional data from simulations of biomolecules to intuitive knowledge is a major challenge in computational chemistry and biology. The so-called "free energy landscape" is amongst the most fundamental…
How useful it is to think about the potential energy landscape of a complex many-body system depends in large measure on how direct the connection is to the system's dynamics. In this paper we show that, within what we call the potential…
This thesis is an attempt to provide a new outlook on complex systems, as well as some physical answers for certain models, taking a computational approach. We have focused on disordered systems, addressing two traditional problems in three…
The equilibrium free energy landscape of off-lattice model heteropolymers as a function of an internal coordinate, namely the end-to-end distance, is reconstructed from out-of-equilibrium steered molecular dynamics data. This task is…
A brief review of modeling and simulation methods for a study of polymers at interfaces is provided. When studying truly multiscale problems as provided by realistic polymer systems, coarse graining is practically unavoidable. In this…
Energy landscapes play a crucial role in shaping dynamics of many real-world complex systems. System evolution is often modeled as particles moving on a landscape under the combined effect of energy-driven drift and noise-induced diffusion,…
The conformational free energy landscape of a system is a fundamental thermodynamic quantity of importance particularly in the study of soft matter and biological systems, in which the entropic contributions play a dominant role. While…
In this paper I describe the computer simulations that I have performed to critically examine the Lauritzen-Hoffman and the Sadler-Gilmer theories of polymer crystallization. In particular, I have computed the free energy profile for…
Predicting phase stabilities of crystal polymorphs is central to computational materials science and chemistry. Such predictions are challenging because they first require searching for potential energy minima and then performing arduous…
We apply a recently proposed criterion for the existence of phase transitions, which is based on the properties of the saddles of the energy landscape, to a simplified model of a system with gravitational interactions, referred to as the…
Monte Carlo computer simulations are used to study the conformational free energy of a folded polymer confined to a long cylindrical tube. The polymer is modeled as a hard-sphere chain. Its conformational free energy $F$ is measured as a…