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Questions tagged [polymers]

Polymers is concerned with the physical properties of individual macromolecules. For questions regarding bulk behavior of ensembles of polymers, the [condensed-matter] tag may be more appropriate.

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The entropic cost of tying knots in polymers

Imagine I take a polymer like polyethylene, of length $L$ with some number of Kuhn lengths $N$, and I tie into into a trefoil knot. What is the difference in entropy between this knotted polymer and a circular polyethylene unknot? Is there an…
TheSheepMan
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Molecular Dynamics Software for Coarse Grained Polymers

I am looking around for MD software that I can use to simulating polymers and I can't decide which software I should use. I would like to simulate the swelling of crosslinked polymers, and I would like to do a coarse grained simulation. The most…
user668074
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Partition function for polymer chain

Supposing that I have linear chain with polymer of $N$ identical particles (interacting harmonically with adjacent particle) with position of first and last particle fixed, how do I find the partition function of the polymer? Here is what I thought,…
S L
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Hindered rotation model for flexible polymers: deriving the Flory characteristic ratio

In the hindered rotation model we assumes constant bond angles $\theta$ and lengths $\ell$, with torsion angles between adjacent monomers being hindered by a potential $U(\phi_i)$. In Rubinstein's book problem 2.9 asks us to derive the Flory…
KBriggs
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Force curve associated with squeezing a worm-like chain (WLC) between two parallel plates

Let's say I have a polymer, of contour length $L_p$ and persistence length $P$, positioned between two parallel plates separated by a distance $z$. I slowly squeeze the plates together until only two-dimensional diffusion is observed. Under the…
TheSheepMan
  • 945
6
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2 answers

Thermodynamics, chaperones: How to model polymer fragmentation?

Living polymers are well described by equilibrium statistical physics. Now I would like to consider a case were living polymers undergo fragmentation due to chaperones. I can think of a kinetic description, but can I still use equilibrium…
J-D
  • 151
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Semiflexible discrete polymer chain

Suppose we have a 2D polymer model described by a set of 2D vectors {$\mathbf{t}_i$} ($i=1,2,\dots N$) of length $a$. The energy of the polymer is given…
molkee
  • 185
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Reference Request - Modern Polymer Dynamics

I'm an applied math graduate student studying the cytoskeleton. I wanted to know of any reference(s) providing the most general mathematical theory of polymer dynamics, think an updated version of Doi & Edwards. This could be a textbook or some…
CasaBonita
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Entropy of a polymer contained in a sphere with infinitely thin chords

Imagine that I have a polymer (approximated as a freely diffusing, freely jointed chain with some number of subunits 'N'), and I place this polymer into a sphere of some volume 'V'. Next, I proceed to add a series of infinitely thin, immobile chords…
MorningCoffee1998
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Pair Correlation Function for ideal polymer chain

I am reading Rubinstein's polymer physics book and on p. 78 it says that if $m$ is the number of monomers within range $r$ of an arbitrary monomer, then $$ m \approx (r/b)^2 $$ where $b$ is the bond length in the chain. The book says that this…
summersfreezing
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What does triviality and non-triviality mean in field theory?

I am studying polymer physics and their basic field theoretical models which has connections to $\Phi ^{4}$ field theory. I frequently come in touch with statements about triviality and non-triviality of the theory with respect to the space…
noisyoscillator
  • 131
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Is a folded protein's conformation subject to thermal fluctuations?

In biology class we learn that proteins are folded, and that the shape the protein takes affects its bioactivity. Typically we don't go much further into protein shape from that, at least not at the level of biology I've taken. Now, my biophysicist…
Dargscisyhp
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Flory-Huggins ternary phase diagram with a neutral component

I am searching the literature for the Flory-Huggins phase diagram with the following components : polymer, solvent, and a third component that does not interact with the other components (just entropy effects). It must have been done but I can't…
J-D
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Exploring potential landscape with Monte Carlo

I am using a Monte Carlo approach for studying folding of a polymer chain. The polymer may fold in many configurations, corresponding to local potential minima, studying which is what interests me (i.e. not only the ground state). Thus, I am…
Roger V.
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Computing microstate probabilities based on Boltzmann distribution for chemical systems - Is it rigorous?

One approach to predicting the folded structure of a polymer (DNA, RNA, protein) is to compute the probability that any particular part of the polymer $x_i$ is "paired" with another part of the polymer $x_j$, per molecule of polymer in a solution at…
Ben Braun
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