伊利諾伊大學(xué)香檳分校(UIUC)的一個(gè)研究小組正在利用聲音來描述生物化學(xué)過程，以幫助科學(xué)家們更好地理解這些過程是如何發(fā)生的。

A team of researchers at the University of Illinois Urbana-Champaign is using sonification – the use of sound to convey information – to depict biochemical processes and better understand how they happen.?

音樂教授&作曲家Stephen Andrew Taylor；美國(guó)科學(xué)院院士，化學(xué)教授&生物物理學(xué)家Martin Gruebele；以及UIUC校友、作曲家和軟件設(shè)計(jì)師Carla Scaletti在UIUC組成了一個(gè)研究小組。自新冠大流行以來，他們每周都會(huì)在Zoom上開會(huì)。該小組正嘗試將蛋白質(zhì)音樂化，以研究蛋白質(zhì)折疊的物理機(jī)制，而這項(xiàng)工作最近有了回報(bào)：Gruebele對(duì)蛋白質(zhì)的折疊方式有了新發(fā)現(xiàn)。

Music?professor and composer?Stephen Andrew Taylor;?chemistry?professor and biophysicist?Martin Gruebele; and Illinois music and computer science alumna, composer and software designer?Carla Scaletti?formed the Biophysics Sonification Group, which has been meeting weekly on Zoom since the beginning of the pandemic. The group has experimented with using sonification in Gruebele’s research into the physical mechanisms of protein folding, and its work recently allowed Gruebele to make a new discovery about the ways a protein can fold.?

Taylor大部分的音樂創(chuàng)作都受到了科學(xué)的影響，他最近的作品融合了大量的科學(xué)數(shù)據(jù)和一些生物學(xué)過程。恰巧，Gruebele院士也是一位音樂家，他建造了自己的管風(fēng)琴并將其用于自身的音樂創(chuàng)作。將科學(xué)事物音樂化的想法讓他們產(chǎn)生了共鳴，并為之進(jìn)行了好幾年的合作。Scaletti用她名下的的公司Symbolic Sound開發(fā)了一個(gè)名為Kyma的數(shù)字音頻軟件和聲音設(shè)計(jì)系統(tǒng)，該系統(tǒng)正被許多音樂家和研究人員使用，包括Taylor。

Taylor’s musical compositions have long been influenced by science, and recent works represent scientific data and biological processes. Gruebele also is a musician who built his own pipe organ that he plays and uses to compose music. The idea of working together on sonification struck a chord with them, and they’ve been collaborating for several years. Through her company, Symbolic Sound Corp., Scaletti develops a digital audio software and hardware sound design system called Kyma that is used by many musicians and researchers, including Taylor.

Scaletti制作了一個(gè)配音動(dòng)畫，用以簡(jiǎn)要說明蛋白質(zhì)的折疊過程。Gruebele和Taylor用該動(dòng)畫來向?qū)W生介紹折疊過程中的那些關(guān)鍵概念，并測(cè)試該動(dòng)畫是否有助于學(xué)生們的理解。他們發(fā)現(xiàn)，將蛋白質(zhì)音樂化這一舉動(dòng)間接加強(qiáng)了其結(jié)構(gòu)的可視化。即使對(duì)專家們來說，音樂化也有助于提高他們對(duì)蛋白質(zhì)折疊和錯(cuò)誤折疊的理解程度。這個(gè)三人小組在《化學(xué)教育雜志》上描述了他們用音樂輔助教學(xué)的過程。DOI: 10.1021/acs.jchemed.1c00857

Scaletti created an animated visualization paired with sound that illustrated a simplified protein-folding process, and Gruebele and Taylor used it to introduce key concepts of the process to students and gauge whether it helped with their understanding. They found that sonification complemented and reinforced the visualizations and that, even for experts, it helped increase intuition for how proteins fold and misfold over time. The Biophysics Sonification Group?described using sonification in teaching?in the?Journal of Chemical Education.

Gruebele和他的研究團(tuán)隊(duì)使用超級(jí)計(jì)算機(jī)對(duì)蛋白質(zhì)折疊成特定結(jié)構(gòu)這一復(fù)雜過程進(jìn)行模擬。模擬顯示了蛋白質(zhì)在折疊過程中的多種途徑，也顯示了它們?nèi)绾握郫B錯(cuò)誤或卡在錯(cuò)誤的形狀中——學(xué)界認(rèn)為，這些錯(cuò)誤與一些疾病有關(guān)，例如阿茨海默癥和帕金森癥。

Gruebele and his research team use supercomputers to run simulations of proteins folding into a specific structure, a process that relies on a complex pattern of many interactions. The simulation reveals the multiple pathways the proteins take as they fold, and also shows when they misfold or get stuck in the wrong shape – something thought to be related to a number of diseases such as Alzheimer’s and Parkinson’s.

(觀看請(qǐng)配合聲音)

視頻一：Martin Gruebele在教學(xué)蛋白質(zhì)折疊動(dòng)力學(xué)的概念時(shí)

使用有聲動(dòng)畫來描述基于簡(jiǎn)單晶格模型的狀態(tài)機(jī)(state machine)

研究人員利用模擬數(shù)據(jù)來深入了解這一過程。據(jù)Gruebele說，幾乎所有的數(shù)據(jù)分析都是以可視化的形式完成的，但是用計(jì)算機(jī)模擬出的大量數(shù)據(jù)可能極其難以可視化：它們包含了數(shù)十萬個(gè)變量和數(shù)百萬個(gè)時(shí)間戳。

The researchers use the simulation data to gain insight into the process. Nearly all data analysis is done visually, Gruebele said, but massive amounts of data generated by the computer simulations – representing hundreds of thousands of variables and millions of moments in time – can be very difficult to visualize.

Scaletti說："在數(shù)字音頻中，一切都是數(shù)據(jù)流，所以實(shí)際上，我們把數(shù)據(jù)流當(dāng)作數(shù)字錄音來聽是很合理的。你可以聽到一些看不見的東西：在數(shù)據(jù)庫(kù)中的信息量如此巨大，總有一些東西是會(huì)被忽視的，但你可以用聲音的形式將它們播放出來。"

“In digital audio, everything is a stream of numbers, so actually it’s quite natural to take a stream of numbers and listen to it as if it’s a digital recording,” Scaletti said. “You can hear things that you wouldn’t see if you looked at a list of numbers and you also wouldn’t see if you looked at an animation. There’s so much going on that there could be something that’s hidden, but you could bring it out with sound.”

例如，當(dāng)?shù)鞍踪|(zhì)折疊時(shí)，它會(huì)被水分子包圍，而水分子對(duì)折疊的過程至關(guān)重要。Gruebele想要知道水分子接觸并將蛋白質(zhì)溶解的具體時(shí)間點(diǎn)，但事實(shí)是，有5萬個(gè)水分子在移動(dòng)，其中只有一兩個(gè)對(duì)溶解起到了關(guān)鍵的作用，以傳統(tǒng)方法觀測(cè)的話，這無異于大海撈針。然而，如果每次水分子接觸到一個(gè)特定的氨基酸時(shí)，就會(huì)出現(xiàn)一個(gè)特殊聲音的話，Gruebele就能輕易找到他想要的時(shí)間點(diǎn)。

For example, when the protein folds, it is surrounded by water molecules that are critical to the process. Gruebele said he wants to know when a water molecule touches and solvates a protein, but “there are 50,000 water molecules moving around, and only one or two are doing a critical thing. It’s impossible to see.” However, if a splashy sound occurred every time a water molecule touched a specific amino acid, that would be easy to hear.

(觀看請(qǐng)配合聲音)

視頻二：蛋白質(zhì)在進(jìn)入折疊狀態(tài)的過程中

會(huì)卡在局部最優(yōu)解?(即局部能量最小值)

Taylor和Scaletti使用音頻映射技術(shù)，將蛋白質(zhì)的各個(gè)特征與聲音參數(shù)聯(lián)系起來，如音高、音色、響度和平移位置。例如，Taylor使用不同的音調(diào)和樂器來代表每個(gè)獨(dú)特的氨基酸，以及它們的疏水性或親水性的程度。

Taylor and Scaletti use various audio-mapping techniques to link aspects of proteins to sound parameters such as pitch, timbre, loudness and pan position. For example, Taylor’s work uses different pitches and instruments to represent each unique amino acid, as well as their hydrophobic or hydrophilic qualities.

"我試圖盡可能地沿用人類對(duì)聲音的本能反應(yīng)，"Taylor說道，"就像貝多芬說的那樣，'水流越深，音調(diào)越低'。我們認(rèn)為大象會(huì)發(fā)出低沉的聲音，因?yàn)樗芫薮螅覀円舱J(rèn)為麻雀會(huì)發(fā)出高亢的聲音，因?yàn)樗苄?。某些特征所?duì)應(yīng)的聲音是扎根在我們的聽覺認(rèn)知里的。我們可以盡可能地利用這些本能認(rèn)知，這有助于設(shè)計(jì)更簡(jiǎn)便的軟件。

“I’ve been trying to draw on our instinctive responses to sound as much as possible,” Taylor said. “Beethoven said, ‘The deeper the stream, the deeper the tone.’ We expect an elephant to make a low sound because it’s big, and we expect a sparrow to make a high sound because it’s small. Certain kinds of mappings are built into us. As much as possible, we can take advantage of those and that helps to communicate more effectively.”

Taylor認(rèn)為，音樂家高度發(fā)達(dá)的音感有助于創(chuàng)造“利用聲音來挖掘信息”的絕佳工具："這是利用音樂和聲音來幫助我們理解世界的新方式。我想音樂家可以在這一過程中發(fā)揮重要作用。與此同時(shí)，我也在努力成為一個(gè)更好的音樂家，在以不同的方式思考聲音如何以不同的方式與整個(gè)世界聯(lián)系，甚至是微觀世界。"

The highly developed instincts of musicians help in creating the best tool to use sound to convey information, Taylor said.?“It’s a new way of showing how music and sound can help us understand the world. Musicians have an important role to play,” he said. “It’s helped me become a better musician, in thinking about sound in different ways and thinking how sound can link to the world in different ways, even the world of the very small.”

轉(zhuǎn)載自:?Illinois News Bureau
"Illinois musicians, chemists use sound to better understand science"

水木視界丨iss. 9