Unifying thermodynamic and kinetic descriptions of single-molecule processes: RNA unfolding under tension

We use mesoscopic non-equilibrium thermodynamics theory to describe RNA unfolding under tension. The theory introduces reaction coordinates, characterizing a continuum of states for each bond in the molecule. The unfolding considered is so slow that one can assume local equilibrium in the space of the reaction coordinates. In the quasi-stationary limit of high sequential barriers, our theory yields the master equation of a recently proposed sequential-step model. Non-linear switching kinetics is found between open and closed states. Our theory unifies the thermodynamic and kinetic descriptions and offers a systematic procedure to characterize the dynamics of the unfolding processComment: 13 pages, 3 figure

Advanced tools and techniques to add value to soil stabilization practice

The aim of this paper is to demonstrate the advanced tools and techniques used for adding value to the soil stabilization practice. The tools presented involve advanced laboratory tests and modeling using codes and soft computing to evaluate the mechanical behavior of stabilized soils with cement, ranging from short-term to long-term behavior. More precisely, these tools are able to: 1. Predict the mechanical behavior of the stabilized soils over time from data obtained in the early ages saving time in laboratory tests; 2. Predict the mechanical behavior of the stabilized soils over time based on basic parameters of soil type and binder using historical accurate data, avoiding mechanical laboratory tests. 3. Incorporate the serviceability limit state concept in a novel proposal to estimate the design modulus in function of the uniaxial compressive strength and the strain level, making more economic and sustainable geotechnical solutions.This work was supported by FCT—‘‘Fundação para a Ciência e a Tecnologia’’, within ISISE, project UID/ECI/04029/2013 and through the post doctoral Grant fellowship with reference SFRH/BPD/94792/2013. This work was also partly financed by FEDER funds through the Competitivity Factors Operational Programme—COMPETE and by national funds through FCT within the scope of the project POCI-01-0145-FEDER-007633.info:eu-repo/semantics/publishedVersio

Statistical mechanics of RNA folding: importance of alphabet size

We construct a minimalist model of RNA secondary-structure formation and use it to study the mapping from sequence to structure. There are strong, qualitative differences between two-letter and four or six-letter alphabets. With only two kinds of bases, there are many alternate folding configurations, yielding thermodynamically stable ground-states only for a small set of structures of high designability, i.e., total number of associated sequences. In contrast, sequences made from four bases, as found in nature, or six bases have far fewer competing folding configurations, resulting in a much greater average stability of the ground state.Comment: 7 figures; uses revtex

Statistical mechanics of secondary structures formed by random RNA sequences

The formation of secondary structures by a random RNA sequence is studied as a model system for the sequence-structure problem omnipresent in biopolymers. Several toy energy models are introduced to allow detailed analytical and numerical studies. First, a two-replica calculation is performed. By mapping the two-replica problem to the denaturation of a single homogeneous RNA in 6-dimensional embedding space, we show that sequence disorder is perturbatively irrelevant, i.e., an RNA molecule with weak sequence disorder is in a molten phase where many secondary structures with comparable total energy coexist. A numerical study of various models at high temperature reproduces behaviors characteristic of the molten phase. On the other hand, a scaling argument based on the extremal statistics of rare regions can be constructed to show that the low temperature phase is unstable to sequence disorder. We performed a detailed numerical study of the low temperature phase using the droplet theory as a guide, and characterized the statistics of large-scale, low-energy excitations of the secondary structures from the ground state structure. We find the excitation energy to grow very slowly (i.e., logarithmically) with the length scale of the excitation, suggesting the existence of a marginal glass phase. The transition between the low temperature glass phase and the high temperature molten phase is also characterized numerically. It is revealed by a change in the coefficient of the logarithmic excitation energy, from being disorder dominated to entropy dominated.Comment: 24 pages, 16 figure