J P Dal Molin - Academia.edu (original) (raw)
Papers by J P Dal Molin
The European Physical Journal E, 2006
We investigate a finite chain approximation, the non-Gaussian Tsallis distribution, to the polyme... more We investigate a finite chain approximation, the non-Gaussian Tsallis distribution, to the polymeric network, which gives an improvement to the Gaussian model. This distribution presents some necessary characteristics, like a cutoff to the maximum chain length and a continuous limit to the Gaussian one for a large number of monomers. It also presents a simple quadratic structure that allows to generalize the Gaussian properties such as exact-moments calculation and Wick theorem. We obtain the free-energy density in its full tensorial structure.
Physica A: Statistical Mechanics and its Applications, 2018
We assume that the protein folding process follows two autonomous steps: the conformational searc... more We assume that the protein folding process follows two autonomous steps: the conformational search for the native, mainly ruled by the hydrophobic effect; and, the final adjustment stage, which eventually gives stability to the native. Our main tool of investigation is a 3D lattice model provided with a ten-letter alphabet, the stereochemical model. This model was conceived for Monte Carlo (MC) simulations when one keeps in mind the kinetic behavior of protein-like chains in solution. In order to characterize the folding characteristic time (τ) by two distinct sampling methods, first we present two sets of 10 3 MC simulations for a fast protein-like sequence. For these sets of folding times, τ and τ q were obtained with the application of the standard Metropolis algorithm (MA), and a modified algorithm (M q A). The results for τ q reveal two things: i) the hydrophobic chain-solvent interactions plus a set of inter-residues steric constraints are enough to emulate the first stage of the process: for each one of the 10 3 MC performed simulations, the native is always found without exception, ii) the ratio τ q /τ≅1/3 suggests that the effect of local thermal fluctuations, encompassed by the Tsallis weight, provides an innate efficiency to the chain escapes from energetic and steric traps. A physical insight is provided. Our second result was obtained through a set of 600 independent MC simulations performed with the M q A method applied to a set of 200 representative targets (native structures). The results show how structural patterns modulate τ q , which cover four orders of magnitude in the temporal scale. The third, and last result, was obtained from a special kind of simulation for those same 200 targets, we simulated their stability. We obtained a strong correlation (R=0.85) between the hydrophobic component of protein stability and the folding rate: the faster is the protein to find the native, larger is the hydrophobic component of its stability. This final result suggests that the hydrophobic interactions could not be a general stabilizing factor for proteins.
Brazilian Journal of Physics, 2009
A reduced (stereo-chemical) model is employed to study kinetic aspects of globular protein foldin... more A reduced (stereo-chemical) model is employed to study kinetic aspects of globular protein folding process, by Monte Carlo simulation. Nonextensive statistical approach is used: transition probability p i j between configurations i → j is given by p i j = [1 + (1 − q)∆G i j /k B T ] 1/(1−q) , where q is the nonextensive (Tsallis) parameter. The system model consists of a chain of 27 beads immerse in its solvent; the beads represent the sequence of amino acids along the chain by means of a 10-letter stereo-chemical alphabet; a syntax (rule) to design the amino acid sequence for any given 3D structure is embedded in the model. The study focuses mainly kinetic aspects of the folding problem related with the protein folding time, represented in this work by the concept of first passage time (FPT). Many distinct proteins, whose native structures are represented here by compact self avoiding (CSA) configurations, were employed in our analysis, although our results are presented exclusively for one representative protein, for which a rich statistics was achieved. Our results reveal that there is a specific combinations of value for the nonextensive parameter q and temperature T, which gives the smallest estimated folding characteristic time t. Additionally, for q = 1.1, t stays almost invariable in the range 0.9 ≤ T ≤ 1.3, slightly oscillating about its average value t = 27 ±σ, where σ = 2 is the standard deviation. This behavior is explained by comparing the distribution of the folding times for the Boltzmann statistics (q → 1), with respect to the nonextensive statistics for q = 1.1, which shows that the effect of the nonextensive parameter q is to cut off the larger folding times present in the original (q → 1) distribution. The distribution of natural logarithm of the folding times for Boltzmann statistics is a triple peaked Gaussian, while, for q = 1.1 (Tsallis), it is a double peaked Gaussian, suggesting that a log-normal process with two characteristic times replaced the original process with three characteristic times. Finally we comment on the physical meaning of the present results, as well its significance in the near future works.
Brazilian Journal of Physics, Aug 1, 2009
A reduced (stereo-chemical) model is employed to study kinetic aspects of globular protein foldin... more A reduced (stereo-chemical) model is employed to study kinetic aspects of globular protein folding process, by Monte Carlo simulation. Nonextensive statistical approach is used: transition probability pij between configurations i→ j is given by pij=[1+(1-q) ΔGi j/kB T] 1/(1-q), where q is the nonextensive (Tsallis) parameter.
Physical Review E, Oct 3, 2011
The series of events that drive a polypeptide chain into its stable native structure is not yet f... more The series of events that drive a polypeptide chain into its stable native structure is not yet fully understood. Protein systems involve so numerous complex interactions and remarkable properties that they continuously require new experiments, as well as theoretical and computational approaches [1–5].
The European Physical Journal E, 2006
We investigate a finite chain approximation, the non-Gaussian Tsallis distribution, to the polyme... more We investigate a finite chain approximation, the non-Gaussian Tsallis distribution, to the polymeric network, which gives an improvement to the Gaussian model. This distribution presents some necessary characteristics, like a cutoff to the maximum chain length and a continuous limit to the Gaussian one for a large number of monomers. It also presents a simple quadratic structure that allows to generalize the Gaussian properties such as exact-moments calculation and Wick theorem. We obtain the free-energy density in its full tensorial structure.
Physica A: Statistical Mechanics and its Applications, 2018
We assume that the protein folding process follows two autonomous steps: the conformational searc... more We assume that the protein folding process follows two autonomous steps: the conformational search for the native, mainly ruled by the hydrophobic effect; and, the final adjustment stage, which eventually gives stability to the native. Our main tool of investigation is a 3D lattice model provided with a ten-letter alphabet, the stereochemical model. This model was conceived for Monte Carlo (MC) simulations when one keeps in mind the kinetic behavior of protein-like chains in solution. In order to characterize the folding characteristic time (τ) by two distinct sampling methods, first we present two sets of 10 3 MC simulations for a fast protein-like sequence. For these sets of folding times, τ and τ q were obtained with the application of the standard Metropolis algorithm (MA), and a modified algorithm (M q A). The results for τ q reveal two things: i) the hydrophobic chain-solvent interactions plus a set of inter-residues steric constraints are enough to emulate the first stage of the process: for each one of the 10 3 MC performed simulations, the native is always found without exception, ii) the ratio τ q /τ≅1/3 suggests that the effect of local thermal fluctuations, encompassed by the Tsallis weight, provides an innate efficiency to the chain escapes from energetic and steric traps. A physical insight is provided. Our second result was obtained through a set of 600 independent MC simulations performed with the M q A method applied to a set of 200 representative targets (native structures). The results show how structural patterns modulate τ q , which cover four orders of magnitude in the temporal scale. The third, and last result, was obtained from a special kind of simulation for those same 200 targets, we simulated their stability. We obtained a strong correlation (R=0.85) between the hydrophobic component of protein stability and the folding rate: the faster is the protein to find the native, larger is the hydrophobic component of its stability. This final result suggests that the hydrophobic interactions could not be a general stabilizing factor for proteins.
Brazilian Journal of Physics, 2009
A reduced (stereo-chemical) model is employed to study kinetic aspects of globular protein foldin... more A reduced (stereo-chemical) model is employed to study kinetic aspects of globular protein folding process, by Monte Carlo simulation. Nonextensive statistical approach is used: transition probability p i j between configurations i → j is given by p i j = [1 + (1 − q)∆G i j /k B T ] 1/(1−q) , where q is the nonextensive (Tsallis) parameter. The system model consists of a chain of 27 beads immerse in its solvent; the beads represent the sequence of amino acids along the chain by means of a 10-letter stereo-chemical alphabet; a syntax (rule) to design the amino acid sequence for any given 3D structure is embedded in the model. The study focuses mainly kinetic aspects of the folding problem related with the protein folding time, represented in this work by the concept of first passage time (FPT). Many distinct proteins, whose native structures are represented here by compact self avoiding (CSA) configurations, were employed in our analysis, although our results are presented exclusively for one representative protein, for which a rich statistics was achieved. Our results reveal that there is a specific combinations of value for the nonextensive parameter q and temperature T, which gives the smallest estimated folding characteristic time t. Additionally, for q = 1.1, t stays almost invariable in the range 0.9 ≤ T ≤ 1.3, slightly oscillating about its average value t = 27 ±σ, where σ = 2 is the standard deviation. This behavior is explained by comparing the distribution of the folding times for the Boltzmann statistics (q → 1), with respect to the nonextensive statistics for q = 1.1, which shows that the effect of the nonextensive parameter q is to cut off the larger folding times present in the original (q → 1) distribution. The distribution of natural logarithm of the folding times for Boltzmann statistics is a triple peaked Gaussian, while, for q = 1.1 (Tsallis), it is a double peaked Gaussian, suggesting that a log-normal process with two characteristic times replaced the original process with three characteristic times. Finally we comment on the physical meaning of the present results, as well its significance in the near future works.
Brazilian Journal of Physics, Aug 1, 2009
A reduced (stereo-chemical) model is employed to study kinetic aspects of globular protein foldin... more A reduced (stereo-chemical) model is employed to study kinetic aspects of globular protein folding process, by Monte Carlo simulation. Nonextensive statistical approach is used: transition probability pij between configurations i→ j is given by pij=[1+(1-q) ΔGi j/kB T] 1/(1-q), where q is the nonextensive (Tsallis) parameter.
Physical Review E, Oct 3, 2011
The series of events that drive a polypeptide chain into its stable native structure is not yet f... more The series of events that drive a polypeptide chain into its stable native structure is not yet fully understood. Protein systems involve so numerous complex interactions and remarkable properties that they continuously require new experiments, as well as theoretical and computational approaches [1–5].