Biomedical subjects

G T Barkema

Publications and source records attributed to G T Barkema.

12 recordsLinked to original sources

PubMed2006

Physical-chemistry-based analysis of affymetrix microarray data.

We analyze publicly available data on Affymetrix microarray spike-in experiments on the human HGU133 chipset in which sequences are added in solution at known concentrations. The spike-in set contains sequences of bacterial, human, and artificial origin. Our analysis is based on a recently introduced molecular-based model (Carlon, E.; Heim, T. Physica A 2006, 362, 433) that takes into account both probe-target hybridization and target-target partial hybridization in solution. The hybridization free energies are obtained from the nearest-neighbor model with experimentally determined parameters. The molecular-based model suggests a rescaling that should result in a "collapse" of the data at different concentrations into a single universal curve. We indeed find such a collapse, with the same parameters as obtained previously for the older HGU95 chip set. The quality of the collapse varies according to the probe set considered. Artificial sequences, chosen by Affymetrix to be as different as possible from any other human genome sequence, generally show a much better collapse and thus a better agreement with the model than all other sequences. This suggests that the observed deviations from the predicted collapse are related to the choice of probes or have a biological origin rather than being a problem with the proposed model.

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PubMed2006

Spinodal decomposition via surface diffusion in polymer mixtures.

We present experimental results for spinodal decomposition in polymer mixtures of gelatin and dextran. The domain growth law is found to be consistent with t 1/4 growth over extended time regimes. Similar results are obtained from lattice simulations of a polymer mixture. This slow growth arises due to the suppression of the bulk mobility of polymers. In that case, spinodal decomposition is driven by the diffusive transport of material along domain interfaces, which gives rise to a t 1/4 growth law.

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PubMed2006

Comment on "Solving the riddle of the bright mismatches: labeling and effective binding in oligonucleotide arrays".

In a recent paper [Phys. Rev. E 68, 011906 (2003)], Naef and Magnasco suggested that the "bright" mismatches observed in Affymetrix microarray experiments are caused by the fluorescent molecules used to label RNA target sequences, which would impede target-probe hybridization. Their conclusion is based on the observation of "unexpected" asymmetries in the affinities obtained by fitting microarray data from publicly available experiments. We point out here that the observed asymmetry is due to the inequivalence of RNA and DNA, and that the reported affinities are consistent with stacking free energies obtained from melting experiments of unlabeled nucleic acids in solution. The conclusion of Naef and Magnasco is therefore based on an unjustified assumption.

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PubMed2005

Activated sampling in complex materials at finite temperature: the properly obeying probability activation-relaxation technique.

While the dynamics of many complex systems is dominated by activated events, there are very few simulation methods that take advantage of this fact. Most of these procedures are restricted to relatively simple systems or, as with the activation-relaxation technique (ART), sample the conformation space efficiently at the cost of a correct thermodynamical description. We present here an extension of ART, the properly obeying probability ART (POP-ART), that obeys detailed balance and samples correctly the thermodynamic ensemble. Testing POP-ART on two model systems, a vacancy and an interstitial in crystalline silicon, we show that this method recovers the proper thermodynamical weights associated with the various accessible states and is significantly faster than molecular dynamics in the simulations of a vacancy below 700 K.

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PubMed2005

Phase separation driven by surface diffusion: a Monte Carlo study.

We propose a kinetic Ising model to study phase separation driven by surface diffusion. This model is referred to as Model S, and consists of the usual Kawasaki spin-exchange kinetics (Model B) in conjunction with a kinetic constraint. We use multispin coding techniques to develop fast algorithms for Monte Carlo simulations of Models B and S. We use these algorithms to study the late stages of pattern dynamics in these systems, and compare properties of the evolution morphologies, e.g., growth laws, domain distribution functions, and spatial and temporal correlation functions.

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PubMed2005

Nucleation times in the two-dimensional Ising model.

We consider the distribution of nucleation times in systems with Brownian type dynamics, as described by classical nucleation theory. This is studied for a prototype system: the two-dimensional Ising model with spin-flip dynamics in an external magnetic field. Direct simulation results for the nucleation times, spanning more than four orders of magnitude, are compared with theoretical predictions. In contrast to usual treatments we determine size-dependent droplet free energies and effective transition rates for growth and shrinkage directly from our simulations. The free energies so determined are well described by the classical Becker-Do ring expression, provided one uses an effective surface tension that exceeds the macroscopic surface tension by up to 20%. Within this framework there is good agreement between simulation results and theoretical predictions for the mean nucleation time. In addition we consider the short-time behavior of the nucleation probability after an initial quench into the metastable state. We present theoretical estimates and show that these too agree well with simulation results.

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PubMed2003

Universality in the pair contact process with diffusion.

The pair contact process with diffusion is studied by means of multispin Monte Carlo simulations and density matrix renormalization group calculations. Effective critical exponents are found to behave nonmonotonically as functions of time or of system length and extrapolate asymptotically towards values consistent with the directed percolation universality class. We argue that an intermediate regime exists where the effective critical dynamics resembles that of a parity conserving process.

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PubMed2003

Magnetization reversal times in the two-dimensional Ising model.

We present a theoretical framework which is generally applicable to the study of time scales of activated processes in systems with Brownian type dynamics. This framework is applied to a prototype system: magnetization reversal times in the two-dimensional Ising model. Direct simulation results for the magnetization reversal times, spanning more than five orders of magnitude, are compared with theoretical predictions; the two agree in most cases within 20%.

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PubMed2002

Configurational entropy of network-forming materials.

We present a computationally efficient method to calculate the configurational entropy of network-forming materials. The method requires only the atomic coordinates and bonds of a single well-relaxed configuration. This is in contrast to the multiple simulations that are required for other methods to determine entropy, such as thermodynamic integration. We use our method to obtain the configurational entropy of well-relaxed networks of amorphous silicon and vitreous silica. For these materials we find configurational entropies of 0.93k(B) and 0.88k(B) per silicon atom, respectively.

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PubMed2001

Diffusion with random distribution of static traps.

The survival probability P(c,t) of a random walk of t steps with static traps at concentration c is studied in two and three dimensions by an efficient Monte Carlo method based on a mapping onto a polymer model. On the basis of the theoretical work of Donsker and Varadhan [Commun. Pure Appl. Math. 28, 525 (1975); 32, 721 (1979)] and of Rosenstock [J. Math. Phys. (N.Y.) 11, 487 (1970)] one expects a data collapse for -ln[P(c,t)]/ln(t) plotted vs square root of [lambda t]/ln(t) [with lambda = -ln(1-c)], in two dimensions, and for -t(-1/3)ln[P(c,t)] vs t(2/3)lambda in three dimensions. These predictions are well supported by the Monte Carlo results.

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PubMed2001

Equilibrium crystal shapes in the Potts model.

The three-dimensional q-state Potts model, forced into coexistence by fixing the density of one state, is studied for q=2, 3, 4, and 6. As a function of temperature and number of states, we studied the resulting equilibrium droplet shapes. A theoretical discussion is given of the interface properties at large values of q. We found a roughening transition for each of the numbers of states we studied, at temperatures that decrease with increasing q, but increase when measured as a fraction of the melting temperature. We also found equilibrium shapes closely approaching a sphere near the melting point, even though the three-dimensional Potts model with three or more states does not have a phase transition with a diverging length scale at the melting point.

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PubMed2001

Sampling activated mechanisms in proteins with the activation-relaxation technique.

The activated dynamics of proteins occur on time scales of milliseconds and longer. Standard all-atom molecular dynamics simulations are limited to much shorter times, of the order of tens of nanoseconds. Therefore, many activated mechanisms that are crucial for long-time dynamics will not be observed in such molecular dynamics simulation; different methods are required. Here, we describe in detail the activation-relaxation technique (ART) that generates directly activated mechanisms. The method is defined in the configurational energy landscape and defines moves in a two step fashion: (a) a configuration is first brought from a local minimum to a nearby first-order saddle point (the activation); and (b) the configuration is relaxed to a new metastable state (the relaxation). The method has already been applied to a wide range of problems in condensed matter, including metallic glasses, amorphous semiconductors and silica glass. We review the algorithm in detail, discuss some previously published results and present simulations of activated mechanisms for a two-helix bundle protein using an all-atom energy function.

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