Non-equilibrium dynamics of gene expression and the Jarzynski equality

In order to express specific genes at the right time, the transcription of genes is regulated by the presence and absence of transcription factor molecules. With transcription factor concentrations undergoing constant changes, gene transcription takes place out of equilibrium. In this paper we discuss a simple mapping between dynamic models of gene expression and stochastic systems driven out of equilibrium. Using this mapping, results of nonequilibrium statistical mechanics such as the Jarzynski equality and the fluctuation theorem are demonstrated for gene expression dynamics. Applications of this approach include the determination of regulatory interactions between genes from experimental gene expression data

Generalized-ensemble Monte carlo method for systems with rough energy landscape

We present a novel Monte Carlo algorithm which enhances equilibrization of low-temperature simulations and allows sampling of configurations over a large range of energies. The method is based on a non-Boltzmann probability weight factor and is another version of the so-called generalized-ensemble techniques. The effectiveness of the new approach is demonstrated for the system of a small peptide, an example of the frustrated system with a rugged energy landscape.Comment: Latex; ps-files include

Monte Carlo simulation and global optimization without parameters

We propose a new ensemble for Monte Carlo simulations, in which each state is assigned a statistical weight $1/k$, where $k$ is the number of states with smaller or equal energy. This ensemble has robust ergodicity properties and gives significant weight to the ground state, making it effective for hard optimization problems. It can be used to find free energies at all temperatures and picks up aspects of critical behaviour (if present) without any parameter tuning. We test it on the travelling salesperson problem, the Edwards-Anderson spin glass and the triangular antiferromagnet.Comment: 10 pages with 3 Postscript figures, to appear in Phys. Rev. Lett

Multicanonical Recursions

The problem of calculating multicanonical parameters recursively is discussed. I describe in detail a computational implementation which has worked reasonably well in practice.Comment: 23 pages, latex, 4 postscript figures included (uuencoded Z-compressed .tar file created by uufiles), figure file corrected

An efficient, multiple range random walk algorithm to calculate the density of states

We present a new Monte Carlo algorithm that produces results of high accuracy with reduced simulational effort. Independent random walks are performed (concurrently or serially) in different, restricted ranges of energy, and the resultant density of states is modified continuously to produce locally flat histograms. This method permits us to directly access the free energy and entropy, is independent of temperature, and is efficient for the study of both 1st order and 2nd order phase transitions. It should also be useful for the study of complex systems with a rough energy landscape.Comment: 4 pages including 4 ps fig

Simultaneous Embeddability of Two Partitions

We study the simultaneous embeddability of a pair of partitions of the same underlying set into disjoint blocks. Each element of the set is mapped to a point in the plane and each block of either of the two partitions is mapped to a region that contains exactly those points that belong to the elements in the block and that is bounded by a simple closed curve. We establish three main classes of simultaneous embeddability (weak, strong, and full embeddability) that differ by increasingly strict well-formedness conditions on how different block regions are allowed to intersect. We show that these simultaneous embeddability classes are closely related to different planarity concepts of hypergraphs. For each embeddability class we give a full characterization. We show that (i) every pair of partitions has a weak simultaneous embedding, (ii) it is NP-complete to decide the existence of a strong simultaneous embedding, and (iii) the existence of a full simultaneous embedding can be tested in linear time.Comment: 17 pages, 7 figures, extended version of a paper to appear at GD 201

Dual Magnetic Separator for TRIμ\muP

The TRI$\mu$P facility, under construction at KVI, requires the production and separation of short-lived and rare isotopes. Direct reactions, fragmentation and fusion-evaporation reactions in normal and inverse kinematics are foreseen to produce nuclides of interest with a variety of heavy-ion beams from the superconducting cyclotron AGOR. For this purpose, we have designed, constructed and commissioned a versatile magnetic separator that allows efficient injection into an ion catcher, i.e., gas-filled stopper/cooler or thermal ionizer, from which a low energy radioactive beam will be extracted. The separator performance was tested with the production and clean separation of $^{21}$Na ions, where a beam purity of 99.5% could be achieved. For fusion-evaporation products, some of the features of its operation as a gas-filled recoil separator were tested.Comment: accepted by Nucl.Instr. Meth., final versio

Aspects of Cooling at the TRIμ\muP Facility

The Tri$\mu$P facility at KVI is dedicated to provide short lived radioactive isotopes at low kinetic energies to users. It comprised different cooling schemes for a variety of energy ranges, from GeV down to the neV scale. The isotopes are produced using beam of the AGOR cyclotron at KVI. They are separated from the primary beam by a magnetic separator. A crucial part of such a facility is the ability to stop and extract isotopes into a low energy beamline which guides them to the experiment. In particular we are investigating stopping in matter and buffer gases. After the extraction the isotopes can be stored in neutral atoms or ion traps for experiments. Our research includes precision studies of nuclear $\beta$-decay through $\beta$-$\nu$ momentum correlations as well as searches for permanent electric dipole moments in heavy atomic systems like radium. Such experiments offer a large potential for discovering new physics.Comment: COOL05 Workshop, Galena, Il, USA, 18-23. Sept. 2005, 5 pages, 3 figure

Partition Function Zeros and Finite Size Scaling of Helix-Coil Transitions in a Polypeptide

We report on multicanonical simulations of the helix-coil transition of a polypeptide. The nature of this transition was studied by calculating partition function zeros and the finite-size scaling of various quantities. Estimates for critical exponents are presented.Comment: RevTex, 4 eps-files; to appear in Phys. Rev. Le

Dynamics of gene expression and the regulatory inference problem

From the response to external stimuli to cell division and death, the dynamics of living cells is based on the expression of specific genes at specific times. The decision when to express a gene is implemented by the binding and unbinding of transcription factor molecules to regulatory DNA. Here, we construct stochastic models of gene expression dynamics and test them on experimental time-series data of messenger-RNA concentrations. The models are used to infer biophysical parameters of gene transcription, including the statistics of transcription factor-DNA binding and the target genes controlled by a given transcription factor.Comment: revised version to appear in Europhys. Lett., new titl