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RealScientists | William

@realscientists

13 Apr

Ok so I had a rather hectic evening, but now let's talk about simulating proteins!

First of all, what's a protein?

Protein's are large biological molecules that are responsible for a myriad of different processes in living things. Feel hungry? In pain? Taste something sweet? Feeling an emotion? All of these things are controlled by a vast array of proteins!

Proteins are amazing! Each one is highly specialised to carry out a specific task, what's incredible is that all proteins are made from the same building blocks called amino acids (AAs).

en.wikipedia.org/wiki/Amino_acid

Read 19 tweets

RealScientists | William

@realscientists

13 Apr

https://twitter.com/chembiogeochem/status/1381941333254889476

Great question!

Yes we can usually determine if a calculation will be expensive by assessing a number of parameters ⬇️

https://twitter.com/chembiogeochem/status/1381941333254889476

In the context of QM calculations we have to assess whether the level of theory we are using is appropriate. Perhaps we could use a cheaper ab initio, semi-empirical, or DFT method. The choice depends on the question and system!

Also: basis sets

Without going into too much detail, basis sets help to describe the shape and behaviour of electrons around certain atoms. We can make them really detailed (i.e. model every electron) or just model the important ones (ones involved in bonding etc)

en.wikipedia.org/wiki/Basis_set…

Read 6 tweets

RealScientists | William

@realscientists

13 Apr

https://twitter.com/Cat_Arses/status/1381705179339235329

This is one thing I didn't mention in my MD thread yesterday: solvent models 🧵

https://twitter.com/Cat_Arses/status/1381705179339235329

What's a solvent model? Simply, it's a way we can model processes that take place in solution (we'll use water as an example since it's the most common)

Proteins (large biological molecules) are usually surrounded by water so it's really important that we model these interactions correctly.

(We'll talk a bit more about proteins today)

Read 10 tweets

RealScientists | William

@realscientists

12 Apr

Now that we've (hopefully) recovered from our quick tour of quantum mechanics we'll now look at molecular dynamics (MD) 🧵

https://twitter.com/realscientists/status/1381576241678057472?s=20

At the end of my last thread I mentioned that we often use QM methods when we want high accuracy, but these methods tend to get very computationally expensive as our system size increases.

https://twitter.com/realscientists/status/1381576241678057472?s=20

When studying larger systems the exact QM description of a molecule often isn't necessary and how its dynamics evolve over longer time frames becomes a more relevant.

(this may not always be the case!)

Read 19 tweets

RealScientists | William

@realscientists

12 Apr

So, what is computational chemistry?! The field itself is a subfield of chemistry, incorporating aspects of theoretical chemistry / physics and computer simulations. This allows us as scientists to accurately describe (and predict) the properties of atoms and molecules.

Computational chemistry is broad and draws on many areas of science, notably quantum mechanics (QM), classical mechanics, and thermodynamics. We often draw (both directly and indirectly) on all three of these areas to answer a specific scientific question.

For example, let's say we want to describe the breaking of chemical bonds in a molecule during a chemical reaction. Here it is appropriate to use QM to accurately describe the energies involved with the exchange of electrons.

In this thread we'll dive into QM!

Read 27 tweets

RealScientists | William

@realscientists

30 Mar

So let's talk about sensory perception!

Basic sensory perception involves our 5 senses:
1. Smell
2. Sight
3. Touch
4. Taste
5. Hearing

You may say that all those don't influence how I perceive food but they do!

We know that smell & taste are influential but how do the others come in?

Touch can be done by our hands if we pick up food but it also accounts for how we perceive texture in our mouth!

But touch is super important in the way we experience food, this is why small children will like to pick up and poke unfamiliar or strange-looking food before they will put it in their mouth!