Optical fluid and biomolecule transport with thermal fields

A long standing goal is the direct optical control of biomolecules and water for applications ranging from microfluidics over biomolecule detection to non-equilibrium biophysics. Thermal forces originating from optically applied, dynamic microscale temperature gradients have shown to possess great potential to reach this goal. It was demonstrated that laser heating by a few Kelvin can generate and guide water flow on the micrometre scale in bulk fluid, gel matrices or ice without requiring any lithographic structuring. Biomolecules on the other hand can be transported by thermal gradients, a mechanism termed thermophoresis, thermal diffusion or Soret effect. This molecule transport is the subject of current research, however it can be used to both characterize biomolecules and to record binding curves of important biological binding reactions, even in their native matrix of blood serum. Interestingly, thermophoresis can be easily combined with the optothermal fluid control. As a result, molecule traps can be created in a variety of geometries, enabling the trapping of small biomolecules, like for example very short DNA molecules. The combination with DNA replication from thermal convection allows us to approach molecular evolution with concurrent replication and selection processes inside a single chamber: replication is driven by thermal convection and selection by the concurrent accumulation of the DNA molecules. From the short but intense history of applying thermal fields to control fluid flow and biological molecules, we infer that many unexpected and highly synergistic effects and applications are likely to be explored in the future

Frustration in Biomolecules

Biomolecules are the prime information processing elements of living matter. Most of these inanimate systems are polymers that compute their structures and dynamics using as input seemingly random character strings of their sequence, following which they coalesce and perform integrated cellular functions. In large computational systems with a finite interaction-codes, the appearance of conflicting goals is inevitable. Simple conflicting forces can lead to quite complex structures and behaviors, leading to the concept of "frustration" in condensed matter. We present here some basic ideas about frustration in biomolecules and how the frustration concept leads to a better appreciation of many aspects of the architecture of biomolecules, and how structure connects to function. These ideas are simultaneously both seductively simple and perilously subtle to grasp completely. The energy landscape theory of protein folding provides a framework for quantifying frustration in large systems and has been implemented at many levels of description. We first review the notion of frustration from the areas of abstract logic and its uses in simple condensed matter systems. We discuss then how the frustration concept applies specifically to heteropolymers, testing folding landscape theory in computer simulations of protein models and in experimentally accessible systems. Studying the aspects of frustration averaged over many proteins provides ways to infer energy functions useful for reliable structure prediction. We discuss how frustration affects folding, how a large part of the biological functions of proteins are related to subtle local frustration effects and how frustration influences the appearance of metastable states, the nature of binding processes, catalysis and allosteric transitions. We hope to illustrate how Frustration is a fundamental concept in relating function to structural biology.Comment: 97 pages, 30 figure

Interaction of aluminium hydrolytic species with biomolecules

In this contribution the formation of bioinorganic assemblies between the basic globular protein lysozyme and aqueous aluminium species including Al 13 -mer, Al 30 -mer and colloidal aluminium hydroxide have been explored and comparison made to previous interaction studies performed with bovine serum albumin (BSA). Specific charge-stabilised bioinorganic assemblies involving aluminium species and lysozyme were observed to form in contrast to the gel like structures formed on interaction of BSA with aluminium species. As demonstrated by infrared spectroscopy (structural assignment, 2D correlation spectroscopy), interactions mostly involve acidic surface groups of the proteins (Asp, Glu), with strong complexation and deprotonation in the case of BSA interacting with Al 13 and Al 30 and through hydrogen bonding for lysozyme interacting with the same species and aluminium hydroxide particles interacting with both biomolecules

The wave nature of biomolecules and fluorofullerenes

We demonstrate quantum interference for tetraphenylporphyrin, the first biomolecule exhibiting wave nature, and for the fluorofullerene C60F48 using a near-field Talbot-Lau interferometer. For the porphyrins, which are distinguished by their low symmetry and their abundant occurence in organic systems, we find the theoretically expected maximal interference contrast and its expected dependence on the de Broglie wavelength. For C60F48 the observed fringe visibility is below the expected value, but the high contrast still provides good evidence for the quantum character of the observed fringe pattern. The fluorofullerenes therefore set the new mark in complexity and mass (1632 amu) for de Broglie wave experiments, exceeding the previous mass record by a factor of two.Comment: 5 pages, 4 figure

Quantifying the Reversible Association of Thermosensitive Nanoparticles

Under many conditions, biomolecules and nanoparticles associate by means of attractive bonds, due to hydrophobic attraction. Extracting the microscopic association or dissociation rates from experimental data is complicated by the dissociation events and by the sensitivity of the binding force to temperature (T). Here we introduce a theoretical model that combined with light-scattering experiments allows us to quantify these rates and the reversible binding energy as a function of T. We apply this method to the reversible aggregation of thermoresponsive polystyrene/poly(N-isopropylacrylamide) core-shell nanoparticles, as a model system for biomolecules. We find that the binding energy changes sharply with T, and relate this remarkable switchable behavior to the hydrophobic-hydrophilic transition of the thermosensitive nanoparticles