Related papers: String Method for the Study of Rare Events
The recently introduced nested sampling algorithm allows the direct and efficient calculation of the partition function of atomistic systems. We demonstrate its applicability to condensed phase systems with periodic boundary conditions by…
Simulations with an adaptive time-dependent bias, such as metadynamics, enable an efficient exploration of the conformational space of a system. However, the dynamic information of the system is altered by the bias. With infrequent…
In this paper, which is a revised version of the author's PhD thesis, we analyze two different applications of string theory. In the first part, we focus on four dimensional compactifications of Type II string theories preserving N=1…
We study the energy-landscape network of Lennard-Jones clusters as a model of a glass forming system. We find the stable basins and the first order saddles connecting them, and identify them with the network nodes and links, respectively.…
Free energy calculations based on atomistic Hamiltonians and sampling are key to a first principles understanding of biomolecular processes, material properties, and macromolecular chemistry. Here, we generalize the Free Energy Perturbation…
Stochastic systems often exhibit multiple viable metastable states that are long-lived. Over very long timescales, fluctuations may push the system to transition between them, drastically changing its macroscopic configuration. In realistic…
Several string theories related to QCD in two dimensions are studied. For each of these theories the large $N$ free energy on a (target) sphere of area $A$ is calculated. By considering theories with different subsets of the geometrical…
The numerical quantification of the statistics of rare events in stochastic processes is a challenging computational problem. We present a sampling method that constructs an ensemble of stochastic trajectories that are constrained to have…
These lectures present some topics of string phenomenology and contain two parts. In the first part, I review the possibility of lowering the string scale in the TeV region, that provides a theoretical framework for solving the mass…
An important problem in the analysis of high-dimensional omics data is to identify subsets of molecular variables that are associated with a phenotype of interest. This requires addressing the challenges of high dimensionality, strong…
Transition interface sampling (TIS) and replica exchange TIS (RETIS) are powerful methods for computing rates of rare events inaccessible to straightforward molecular dynamics (MD) simulations. Path reweighting extends their output,…
Intensity distributions of linear wave fields are, in the high frequency limit, often approximated in terms of flow or transport equations in phase space. Common techniques for solving the flow equations for both time dependent and…
We investigate string amplitudes by using the partial modular transformation which we introduced in our previous works. This enables us to extract stringy threshold corrections from the full string amplitudes and interpret them in terms of…
The rare-event sampling problem has long been the central limiting factor in molecular dynamics (MD), especially in biomolecular simulation. Recently, diffusion models such as BioEmu have emerged as powerful equilibrium samplers that…
We analyze the problem of calculating the solutions and the spectrum of a string with arbitrary density and fixed ends. We build a perturbative scheme which uses a basis of WKB-type functions and obtain explicit expressions for the…
We develop computational tools for spectral analysis of stochastic networks representing energy landscapes of atomic and molecular clusters. Physical meaning and some properties of eigenvalues, left and right eigenvectors, and eigencurrents…
Physical systems with many degrees of freedom can often be understood in terms of transitions between a small number of metastable states. For time-homogeneous systems with short-term memory these transitions are fully characterized by a…
Random matrix theory of the transition strengths is applied to transport in the strongly localized regime. The crossover distribution function between the different ensembles is derived and used to predict quantitatively the {\sl universal}…
A strategy for finding transition paths connecting two stable basins is presented. The starting point is the Hamilton principle of stationary action; we show how it can be transformed into a minimum principle through the addition of…
In molecular dynamics (MD) simulations, transitions between states are often rare events due to energy barriers that exceed the thermal temperature. Because of their infrequent occurrence and the huge number of degrees of freedom in…