Cytochemical studies of planetary microorganisms - Explorations in exobiology Status report, 1 Apr. - 1 Oct. 1967

Molecular research instrumentation for exobiological studie

Cytochemical studies of planetary microorganisms - Explorations in exobiology Status report, Sep. 1, 1965 - Apr. 1, 1966

Cytochemical studies of planetary microorganisms by fluorometry, gas chromatography and optical resolution, mass spectrometry, computer managed instrumentation, and UV microspectrometr

Relationship of planetary quarantine to biological search strategy

Decision theory biological search strategies and planetary quarantine aspects of Mars exploratory mission

Contamination of mars

Spacecraft sterilization standards and microbial contamination of Mar

A Criterion That Determines Fast Folding of Proteins: A Model Study

We consider the statistical mechanics of a full set of two-dimensional protein-like heteropolymers, whose thermodynamics is characterized by the coil-to-globular ($T_\theta$) and the folding ($T_f$) transition temperatures. For our model, the typical time scale for reaching the unique native conformation is shown to scale as $\tau_f\sim F(M)\exp(\sigma/\sigma_0)$, where $\sigma=1-T_f/T_\theta$, $M$ is the number of residues, and $F(M)$ scales algebraically with $M$. We argue that $T_f$ scales linearly with the inverse of entropy of low energy non-native states, whereas $T_\theta$ is almost independent of it. As $\sigma\rightarrow 0$, non-productive intermediates decrease, and the initial rapid collapse of the protein leads to structures resembling the native state. Based solely on {\it accessible} information, $\sigma$ can be used to predict sequences that fold rapidly.Comment: 10 pages, latex, figures upon reques

A Multicanonical Molecular Dynamics Study on a Simple Bead-Spring Model for Protein Folding

We have performed a multicanonical molecular dynamics simulation on a simple model protein.We have studied a model protein composed of charged, hydrophobic, and neutral spherical bead monomers.Since the hydrophobic interaction is considered to significantly affect protein folding, we particularly focus on the competition between effects of the Coulomb interaction and the hydrophobic interaction. We found that the transition which occurs upon decreasing the temperature is markedly affected by the change in both parameters and forms of the hydrophobic potential function, and the transition changes from first order to second order, when the Coulomb interaction becomes weaker.Comment: 7 pages, 6 postscript figures, To appear in J.Phys.Soc.Jpn. Vol.70 No.

The effect of local thermal fluctuations on the folding kinetics: a study from the perspective of the nonextensive statistical mechanics

Protein folding is a universal process, very fast and accurate, which works consistently (as it should be) in a wide range of physiological conditions. The present work is based on three premises, namely: ($i$) folding reaction is a process with two consecutive and independent stages, namely the search mechanism and the overall productive stabilization; ($ii$) the folding kinetics results from a mechanism as fast as can be; and ($iii$) at nanoscale dimensions, local thermal fluctuations may have important role on the folding kinetics. Here the first stage of folding process (search mechanism) is focused exclusively. The effects and consequences of local thermal fluctuations on the configurational kinetics, treated here in the context of non extensive statistical mechanics, is analyzed in detail through the dependence of the characteristic time of folding ($\tau$) on the temperature $T$ and on the nonextensive parameter $q$.The model used consists of effective residues forming a chain of 27 beads, which occupy different sites of a $3-$D infinite lattice, representing a single protein chain in solution. The configurational evolution, treated by Monte Carlo simulation, is driven mainly by the change in free energy of transfer between consecutive configurations. ...Comment: 19 pages, 3 figures, 1 tabl

Directed transport as a mechanism for protein folding in vivo

We propose a model for protein folding in vivo based on a Brownian-ratchet mechanism in the multidimensional energy landscape space. The device is able to produce directed transport taking advantage of the assumed intrinsic asymmetric properties of the proteins and employing the consumption of energy provided by an external source. Through such a directed transport phenomenon, the polypeptide finds the native state starting from any initial state in the energy landscape with great efficacy and robustness, even in the presence of different type of obstacles. This model solves Levinthal's paradox without requiring biased transition probabilities but at the expense of opening the system to an external field.Comment: 16 pages, 7 figure

Reply to Comment on "Criterion that Determines the Foldability of Proteins"

We point out that the correlation between folding times and $\sigma = (T_{\theta } - T_{f})/T_{\theta }$ in protein-like heteropolymer models where $T_{\theta }$ and $T_{f}$ are the collapse and folding transition temperatures was already established in 1993 before the other presumed equivalent criterion (folding times correlating with $T_{f}$ alone) was suggested. We argue that the folding times for these models show no useful correlation with the energy gap even if restricted to the ensemble of compact structures as suggested by Karplus and Shakhnovich (cond-mat/9606037).Comment: 6 pages, Latex, 2 Postscript figures. Plots explicitly showing the lack of correlation between folding time and energy gap are adde

Sequence Dependence of Self-Interacting Random Chains

We study the thermodynamic behavior of the random chain model proposed by Iori, Marinari and Parisi, and how this depends on the actual sequence of interactions along the chain. The properties of randomly chosen sequences are compared to those of designed ones, obtained through a simulated annealing procedure in sequence space. We show that the transition to the folded phase takes place at a smaller strength of the quenched disorder for designed sequences. As a result, folding can be relatively fast for these sequences.Comment: 14 pages, uuencoded compressed postscript fil